Gene: 1624 Name: Gria4 Family: Channel Subfamily: Glutamate Gated Accession: AB022913 GI: 4210478
Gene: 1624

Gene 1624
BLASTx Output


BLASTx Output. The query sequence is the Deltagen target gene.  The top "hits" are shown with
accession number, BLAST score and probability.  The alignment of the best hit is also shown.

BLAST DATE : 3/13/2003

 

                                                                         Score    E
 
 
gi|9790091|ref|NP_062665.1|  glutamate receptorionotropic...  1724   0.0  
gi|8393478|ref|NP_058959.1|  glutamate receptorionotropic...  1699   0.0  
gi|4557631|ref|NP_000820.1|  glutamate receptorionotrophic...  1693   0.0  
gi|348418|pir||A44839  glutamate receptor 4c - rat >gi|24711...  1616   0.0  
 
>gi|9790091|ref|NP_062665.1| glutamate receptorionotropicAMPA4 (alpha 4); glutamate receptor
            channel alpha 4 [Mus musculus]
 gi|20138449|sp|Q9Z2W8|GLR4_MOUSE Glutamate receptor 4 precursor (GluR-4) (GluR4) (GluR-D) (Glutamate
            receptor ionotropicAMPA 4)
 gi|4210479|dbj|BAA74538.1| glutamate receptor channel alpha4 subunit [Mus musculus]
          Length = 902
 
 Score = 1724 bits (4465)Expect = 0.0
 
 Identities = 860/902 (95%)Positives = 860/902 (95%)
 Frame = +1
 
Query: 214  MRIICRQIVLLFSGFWGLAMGAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEA 393
            MRIICRQIVLLFSGFWGLAMGAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEA
Sbjct: 1    MRIICRQIVLLFSGFWGLAMGAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEA 60
 
Query: 394  PFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITP 573
            PFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITP
Sbjct: 61   PFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITP 120
 
Query: 574  SFPTEGESQFVLQLRPSLRGALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWH 753
            SFPTEGESQFVLQLRPSLRGALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWH
Sbjct: 121  SFPTEGESQFVLQLRPSLRGALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWH 180
 
Query: 754  VSAICVENFNDVSYRQLLEELDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIA 933
            VSAICVENFNDVSYRQLLEELDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIA
Sbjct: 181  VSAICVENFNDVSYRQLLEELDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIA 240
 
Query: 934  NLGFKDISLERFIHGGANVTGFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSAL 1113
            NLGFKDISLERFIHGGANVTGFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSAL
Sbjct: 241  NLGFKDISLERFIHGGANVTGFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSAL 300
 
Query: 1114 TYDGVLVMAETFRSLRRQKIDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGN 1293
            TYDGVLVMAETFRSLRRQKIDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGN
Sbjct: 301  TYDGVLVMAETFRSLRRQKIDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGN 360
 
Query: 1294 VQFDHYGRRVNYTMDVFELKSTGPRKVGYWNDMDKLVLIQDAPTLGNDTAAIENRTVVVT 1473
            VQFDHYGRRVNYTMDVFELKSTGPRKVGYWNDMDKLVLIQDAPTLGNDTAAIENRTVVVT
Sbjct: 361  VQFDHYGRRVNYTMDVFELKSTGPRKVGYWNDMDKLVLIQDAPTLGNDTAAIENRTVVVT 420
 
Query: 1474 TIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTK 1653
            TIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTK
Sbjct: 421  TIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTK 480
 
Query: 1654 IWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL 1833
            IWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL
Sbjct: 481  IWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL 540
 
Query: 1834 DPLAYEIWMCIVFAYIGXXXXXXXXXXXXPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLW 2013
            DPLAYEIWMCIVFAYIG            PYEWHTEEPEDGKEGPSDQPPNEFGIFNSLW
Sbjct: 541  DPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLW 600
 
Query: 2014 FSLGAFMQQGCDISPRSLSGRIVGGVWWFGTLIIISSYTANLAAFLTVERMVSPIESAED 2193
            FSLGAFMQQGCDISPRSLSGRIVGGVWWFGTLIIISSYTANLAAFLTVERMVSPIESAED
Sbjct: 601  FSLGAFMQQGCDISPRSLSGRIVGGVWWFGTLIIISSYTANLAAFLTVERMVSPIESAED 660
 
Query: 2194 LAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKG 2373
            LAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKG
Sbjct: 661  LAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKG 720
 
Query: 2374 KFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGL 2553
            KFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGL
Sbjct: 721  KFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSSLGNAVNLAVLKLNEQGL 780
 
Query: 2554 LDKLKNKWWYXXXXXXXXXXXXXXXXXALSLSNVAGVFYIXXXXXXXXXXXXXIEFCYKS 2733
            LDKLKNKWWY                 ALSLSNVAGVFYI             IEFCYKS
Sbjct: 781  LDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKS 840
 
Query: 2734 RAEAKRMKLTFSEAIRNKARLSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASD 2913
            RAEAKRMKLTFSEAIRNKARLSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASD
Sbjct: 841  RAEAKRMKLTFSEAIRNKARLSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASD 900
 
Query: 2914 LP 2919
            LP
Sbjct: 901  LP 902
 
 
 

Construct

Gene:

1624

 

GI Number(s):

4210478

ES Cell Line:

5156

 

 

Accession Number:

AB022913

 

 

Family:

Channel

 

 

Subfamily:

Glutamate Gated

 

 

Species:

Mouse

 

 

 

Sequence Type:

full length cDNA

 

 

 

 

 


Sequence Length:

2954 bp

 

red underlined text = deleted in gene sequence

Sequence Deleted:

from base 348 to base 409

 

black text = gene sequence flanking deleted sequence



GAAACATCTGGCAGCTGGGGATGGATTGTTGAGGGAAAGCTGTCATAACCTAAAAGCACC
CAAACCTTTTCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTGAATT
TTAGCGCCATCATCTTCAATGCCTCTCTGAAAATCATTTAGCAAGAGTGAGAGAAAGAGA
GGAGAGCGCGCACCAGGGAGAGGAGCAAAGAAGATGAGGATTATTTGCAGGCAGATTGTC
TTGTTGTTTTCTGGATTTTGGGGACTCGCCATGGGAGCCTTTCCGAGCAGCGTTCAAATA
GGTGGTCTCTTTATCCGAAACACAGACCAGGAATACACTGCTTTTCG
GCTAGCTATCTTT
CTTCATAACACCAGCCCCAATGCATCTGAAGCCCCTTTCAATTTGGTAC
CTCATGTGGAC
AACATTGAGACTGCCAACAGTTTTGCTGTGACAAATGCATTCTGTTCCCAGTATTCTAGA
GGGGTGTTTGCCATTTTTGGACTCTATGACAAGAGGTCAGTGCATACCTTGACCTCCTTC
TGCAGTGCTCTGCACATCTCTCTCATCACACCAAGCTTCCCCACTGAAGGAGAGAGCCAG
TTCGTGCTTCAGCTAAGACCTTCATTGAGAGGTGCACTCCTGAGCCTCCTGGATCACTAT
GAATGGAATTGTTTTGTCTTCCTGTATGATACAGACAGGGGGTATTCAATACTTCAAGCT
ATAATGGAAAAAGCAGGACAGAATGGATGGCATGTCAGTGCGATATGTGTGGAAAATTTT
AACGATGTCAGCTACAGGCAACTACTAGAAGAGCTTGACAGAAGACAAGAGAAGAAATTT
GTAATAGATTGTGAGATAGAAAGGCTTCAAAACATATTAGAACAAATTGTGAGTGTTGGG
AAGCACGTCAAAGGCTACCATTATATCATCGCAAATTTGGGTTTCAAAGATATTTCTCTT
GAGAGATTTATACATGGAGGAGCAAATGTCACTGGATTCCAGTTAGTAGATTTTAATACG
CCCATGGTGACGAAACTAATGGATCGCTGGAAGAAACTAGATCAACGAGAATATCCAGGA
TCTGAAACACCTCCAAAGTACACTTCTGCTCTCACTTACGATGGTGTCTTGGTAATGGCT
GAAACTTTCCGAAGTCTCAGAAGACAGAAAATTGATATTTCAAGGAGAGGAAATGCAGGG
GATTGTCTGGCAAACCCTGCTGCTCCCTGGGGCCAGGGAATTGACATGGAGAGAACACTG
AAGCAGGTTCGAATTCAAGGACTGACTGGGAATGTTCAATTTGACCACTATGGACGTAGA
GTTAATTACACAATGGATGTGTTTGAATTAAAAAGCACAGGACCTCGAAAGGTTGGCTAT
TGGAACGATATGGATAAATTAGTCTTGATTCAAGATGCGCCTACTCTTGGCAATGACACA
GCAGCTATCGAGAACAGAACAGTGGTTGTAACCACAATTATGGAATCCCCCTACGTTATG
TACAAGAAAAATCATGAAATGTTTGAAGGAAATGACAAGTATGAAGGCTACTGTGTAGAC
TTGGCATCTGAAATTGCGAAACATATCGGTATCAAATATAAAATTGCCATTGTCCCTGAT
GGAAAATATGGAGCAAGGGATGCGGACACCAAAATTTGGAATGGGATGGTAGGAGAGCTT
GTGTATGGGAAAGCAGAGATTGCCATTGCACCTCTGACAATCACGTTGGTGCGAGAGGAG
GTCATCGACTTTTCTAAGCCTTTTATGAGTTTAGGCATCTCTATCATGATCAAAAAACCT
CAGAAATCTAAACCAGGCGTGTTTTCCTTCTTGGACCCTCTGGCCTATGAGATCTGGATG
TGCATAGTGTTTGCATACATTGGTGTCAGCGTGGTCTTGTTCCTAGTCAGTAGGTTTAGC
CCATATGAGTGGCACACAGAAGAGCCTGAGGATGGAAAAGAAGGACCCAGTGACCAACCT
CCCAATGAGTTTGGCATCTTTAACAGCCTCTGGTTTTCCCTGGGTGCCTTTATGCAACAA
GGATGTGACATTTCACCCAGATCCCTGTCCGGTCGGATTGTTGGAGGCGTATGGTGGTTC
GGCACTCTCATCATTATCTCATCCTACACTGCTAATCTGGCTGCATTCCTGACAGTGGAG
AGAATGGTCTCCCCCATAGAAAGTGCAGAAGACCTGGCCAAACAAACAGAAATTGCCTAT
GGAACACTTGATTCGGGATCAACAAAAGAATTCTTCAGAAGATCAAAAATAGCAGTATAT
GAAAAGATGTGGACCTACATGCGATCGGCAGAGCCATCTGTGTTCACTAGAACTACAGCT
GAGGGCGTGGCCCGTGTCCGCAAGTCCAAGGGCAAATTTGCCTTCCTCCTGGAGTCCACG
ATGAATGAATACATTGAGCAGCGAAAGCCCTGTGACACGATGAAAGTGGGAGGAAACCTG
GATTCCAAAGGCTATGGTGTAGCGACGCCCAAGGGTTCCTCATTAGGAAATGCTGTTAAC
CTCGCAGTTTTAAAACTGAATGAACAAGGCCTCTTGGACAAATTGAAAAACAAATGGTGG
TACGACAAAGGAGAATGTGGCAGCGGGGGAGGTGACTCCAAGGACAAGACGAGTGCCTTG
AGCCTGAGCAACGTAGCAGGCGTCTTCTACATTCTGGTTGGCGGCTTGGGCTTGGCAATG
CTGGTGGCTTTGATAGAGTTCTGTTACAAGTCCAGGGCAGAGGCGAAGAGAATGAAGCTG
ACTTTTTCCGAAGCCATAAGAAACAAAGCCAGGTTATCCATCACTGGGAGTGTGGGAGAA
AACGGCCGTGTGCTGACCCCCGACTGCCCCAAGGCCGTACACACAGGAACTGCGATTAGA
CAGAGCTCGGGATTGGCTGTCATTGCATCGGACCTACCATAAAAACCAAAAAATTAATTG
AGTGCCTTAATCAA




Targeting Vector* (genomic sequence)

    LacZ-Neo

Construct Number:  10021

Arm Length:
5':  2  kb
3':  4  kb


  * Not drawn to scale



 

5 ' PCR Reconfirmation

Gene:

1624

ES Line:

5156

Gene Specific Oligo (GS):
CCACCTCCAGAGCCGGTTCCTCGGC

32972



Gel

Expected Results and Diagram

 11000bp

 10000bp

 9000bp

 8000bp

 7000bp

 6000bp

 5000bp

 4000bp

 3000bp

 2000bp

 1600bp

 1000bp

 500bp

Lane Number

Label

Expected Size (in bp)

1

1kB Ladder

 

2

32972 + NEO1 (11193)

2125

3

32972 + NEO2 (11192)

2135

4

32972 + NEO3 (2416)

2700

5

DNA Sample Control

5167

6

Positive Control

2000

 


 

3 ' PCR Reconfirmation

Gene:

1624

ES Line:

5156

Gene Specific Oligo (GS):
AAGATATGAATGGTATCAGGCATGG

32969



Gel

Expected Results and Diagram

 11000bp

 10000bp

 9000bp

 8000bp

 7000bp

 6000bp

 5000bp

 4000bp

 3000bp

 2000bp

 1600bp

 1000bp

 500bp

Lane Number

Label

Expected Size (in bp)

1

1kB Ladder

 

2

32969 + NEO1 (1431)

4000

3

32969 + NEO2 (1432)

3950

4

32969 + NEO3 (1170)

3250

5

DNA Sample Control

5167

6

Positive Control

3000

 


 

Legend : Genomic DNA from the recombinant ES line was assayed for homologous recombination using polymerase chain reactions (PCRs). Amplified DNA fragments were visualized by ethidium bromide staining following agarose gel electrophoresis, as shown in the gel image on the left. The test PCRs (a set of three lanes) employed the gene-specific (GS) primer, which lies outside of and adjacent to the targeting vector arm, paired in succession with one of three primers in the insertion fragment. The "DNA sample control" employed a primer pair intended to amplify a fragment from a non-targeted genomic locus. The "positive control" employed the GS primer paired with a primer at the other end of the arm. The table below the gel image lists the primers (numbered) used in each PCR and the expected product sizes, in base pairs (bp).  The diagrams to the right depict the anticipated gel image as well as the relative positions of the PCR primers.

 

 

 

3 ' Southern Blot Confirmation

Gene:

1624

ES Line:

5156

Construct:

10021

Blot Number:

5073

Gene Side:

3'

 

 

MW Marker

Lane

ES Line

Enzyme

 

1

Parent 1

Bgl II

 

2

Parent 2

Bgl II

 

3

5156

Bgl II

 

Legend : Genomic DNA isolated from the indicated ES lines was digested with the indicated restriction enzymes (determined to cut outside of the construct arms).  The DNA was analyzed by Southern hybridization, probing with a radiolabeled DNA fragment that hybridizes outside of and adjacent to the construct arm.  The parent ES lines (negative controls) showed bands representing the endogenous (wild-type) Gene #1624 allele.  In contrast, the ES#5156  line showed an additional band representing the targeted allele from the expected homologous recombination event.  
Note: All lanes represent data from the same blot.