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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag

Basic information

species Arabidopsis thaliana
transcript AT1G24180.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctt----tgttcatttgtaaga-ctactgctccaacc--atatgcaattt-----gaaactttttaatctg--taaagttttcat-cggtgttacctttag
|| |||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||| ||  | ||||||||  | ||| | |||||||| ||   |     ||  |     | ||  ||   |   | ||   | |   |||||     |||    || | ||||  |||  | ||  |    |||||||   ||
ATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAGgtcaggaatcaggatggccggccatgagctctcgagtctcgactcaaaacttaatttacaccgaagacattcattctgagtaagttgtttgtgttatgttaccaacag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag
 | ||||| ||||| || ||||| ||||| || || |||||||| || || |||||||||||||||||  | ||||| ||||| || || |||||||| ||     |||       | | | |  || |  ||  |    ||  |      |||||||    | |   ||| |||  ||  | |     
GTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAGgtgaggatcctgt--gacccttaaatttgtggtgtaattaacgccagatgtttggtttttaacgaattattgttttatca-tgccaacag---

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G361693_T01 (Zea mays), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag
 ||||||||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||| ||  | ||||| || || || || || ||||| || |  || || || | | ||  |     |  || |||        ||   |  || | | ||| |   | ||||| |            
GTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAGgtaaggttgtt-ttgatctttcagtatggaatttaaagcatgctatgcgtgtttcaattaattgtgttacaatatcatcag------------

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G027627_T01 (Zea mays), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttag--------ttctttgttcatttgtaagac-tactgctccaaccatatgcaatttgaaactttt------taatctgtaaagttttcatcggtgttacctttag
||||||||||||||||| |||||||||||||| ||||| ||||| || ||||| ||||| ||||| ||  | ||||| ||| ||||| | || ||||| ||        || | |   || |||  | |  |  | |||     ||   ||||||     | ||      | ||||||   || | |     | | ||    ||
ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAGgtcaggatggcagttgtctcggcacttgagaaatgtgttcctcaggggatgaacaatttttttttctttctgaatgatctgtct-gtctacggaattatgacacacag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G140150_T01 (Zea mays), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag
 ||||||||||||| || ||||| ||||| || ||||||||||| || ||||||||||||||||| ||  | ||||| || || || || || |||||  | |  || || || | | ||  |     |  || |||     |  ||  ||  || | ||||| |   | ||||| |            
GTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAGgtatgattgtt-ttaatctttcagtttggaatttaaatcatgatataagtgttacaattaattctgttacaatatcatcag------------

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G04470.1 (Glycine max), 5'ss of exon 2
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagtt-ctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag--
|| ||||| |||||||||||||||||||| || |||||||||||||| |  || ||||| |||||||| ||||||||||| ||||| |||||||||||| ||  |  |  ||       | || | | ||  |    | | | ||||  |    |||  | |   || ||||| | | || ||   ||    
ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAGgtttgtcacactagtc--ccagcatacaatttctt-atttgtttactattttgagaaatttgttttaataatttttcttggctgatataattgtag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagtt-ctttgttcatttgtaagactactgctccaaccatatgcaattt-gaaactttttaatctgtaaagttttcatcggtgttacctttag--
|| ||||| |||||||||||||||||||| || |||||||||||||| || || ||||| ||||| || ||||||||||| ||||| |||||||||||| ||  |  |  ||    | |  || | | ||  |    | | |  ||| || |  |||   |   ||   ||||| | | || ||   ||    
ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAGgtttgtcacactagtccccagcat-acaatttctt-attagtttacttttttgagaaatttgttttaatatttttttcttggctgatataattgtag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G40380.1 (Glycine max), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgt-tagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactt-tttaatctgtaaagttttc--atcggtgttacctttag
|| ||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||| |||||||| |||||||| || ||||| ||||||||||| |  | || || ||||    ||   |  |  |      ||    | |  | |  ||  |  |||| | |  || ||   ||     |   |  ||
ATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAGgtatcttactatgatcataatcaaatgtcttatttgtttaattaatattgaggagtttactctatcttttattttctcctgtccaatctgattacag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G17240.1 (Glycine max), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgt-tagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactt-tttaatctgtaaagttttcatcggtgttacct--ttag--
|| || ||||||||||| ||||||||||| || ||||| |||||||| || || ||||| |||||||| |||||||| || ||||| || |||||||| || | || |  ||||   |||   | ||  |      ||    | |  | |  ||  |  |||| |    |||||  | ||   | ||  |||   
ATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAGgtatattactataatcataattaaatgtcctatttgtttaattaatattgaggagtttactctatctcttttattttctcctgtccaatctgattatag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgt-----tagttctttgtt--catttgtaagactactgctccaaccatatgcaattt---gaaactttttaatctgtaaagttttcatcggtgttacctttag
|| ||||| ||||||||||| || ||||| |||||||| |||||||| || || ||||| |||||||| |||||||| || ||||| |||||||||||     |  |    | ||  ||||| |  |  | ||||        |   ||||||     || ||       |  ||  ||||    ||| |    | |||
ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAGgtgtatatgatatgatattgacatttttttgtttgctgcaaagcgtgttatcaatttcctagaagttccatgcattaaatatttttggtggtatgttttctag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgt-ta-gttctttgttc-----atttgtaagactactgctccaaccatatgcaattt---gaaactttttaatctgtaaagttttcatcggtgttacctttag
|| ||||| ||||||||||| || ||||| |||||||| |||||||| || || || || |||||||| |||||||| || ||||| ||||||||||| ||  | || || ||     |||| |  |  | ||||        |   ||||||   | || |||    | |  ||   |||    ||  |    | |||
ATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAGgtgtatatgctatgatcttgacatttttttgtttgctgcagtgtgtgttgacaatttcctggaagtttcatgtattaaatagttttggtggcatgttttctag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S47_1V6.1 (Physcomitrella patens), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctccaaccatatgcaatttgaaactttttaatctgtaaagtttt--catcggtgttacctttag-------------------------------------------------------------
 || | ||||||||||| || || || || || || || ||||| |||||||| ||||||||||| |||||||| || |||||||| ||  | || || ||||     |  | |||      |     |     || ||   ||   ||  |    ||| |  || | |||   |  |  ||||    |                                                               
GTCTTGGAGATGGACACATATAGGTATCATGGACATTCCATGTCCGACCCAGGCAGCACTTACCGAACTCGTGACGAGATCTCTGGTGTTCGTCAAgtaagtttcagttgaacttgctcttttcgaagttagcacaaattacatggaaagatgaccaatttacaaggatttggtactgcggttattgctcaagtatgctgttggtgaccagactatgttttcagtctaacatctttctactcgtgtcaacag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcatttgtaagactactgctcc--aaccatatgcaatttgaaactttttaatctgtaaagttttcatcggtgttacctttag----------------------------------
 |  | |||||||| || |||||||| || ||||||||||||||||||||||| ||||| ||||| || |||||||| |||||||| ||  |||||||  | |  |  |  | ||| | |   |||||     |||  | | |  || | |   | || || |||      |   | | ||  |||   |                                   
GTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAGgtgtgattctaatcaagttg-acgttcactgcattgaaactgttttcggttaggagggtattgat-tgtttgccctgagttgctgagacccagatttattttcttacacttttttgctgatgtatacag

upper sequence: AT1G24180.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S56_222V6.1 (Physcomitrella patens), 5'ss of exon 4
ATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctttgttcat-ttgtaaga-ctactgctccaaccatatg---caatttgaaactttttaatctgtaaagttttcatcggtg--ttacctttag--------------------------------------------------
 |  | |||||||||||||| || || || ||||||||||||||||||||||| ||||| || || |||||||| || ||||| || ||  |||||||  | |     | ||| |||| | |  | |||  |    | |  |      ||| |        ||   ||  | || |  |  |||  ||    | |                                                   
GTTTTGGAGATGGACACTTATAGGTATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTATCGAACTCGTGACGAGATCTCCGGTGTCCGACAGgtgtgcttccactccatgttgtgaaagtttctgtgcgctgcgttggggttgctttcagttcaaagaactcgttgatttcttttttgtgacttgtgctgaaatgaccagaccaaggttcacttatgtaatcccttattcttatgcgtatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116467475|gb|EG510067.1|EG510067
EST:     ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG                         GTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
genomic: ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctt ... ttacctttagGTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
EST: gi|116486096|gb|EG528688.1|EG528688
EST:     ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG                         GTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
genomic: ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctt ... ttacctttagGTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
EST: gi|47828819|gb|CK118503.1|CK118503
EST:     ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG                         GTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
genomic: ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctt ... ttacctttagGTGCGTGATCCAATTGAAAGGGTGCGAAAGTTGCTCTTAACTCATGACATA
EST: gi|116465222|gb|EG507814.1|EG507814
EST:     ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG                         GTGCGTGATCCAATTTGAAAGGGTGCGAAA
genomic: ACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAGgttagttctt ... ttacctttagGTGCGTGATCCAATT-GAAAGGGTGCGAAA