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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttattaattctgtttatatatttattcattattgttcctatatagtatatttttgtgtttttttattcttcatctatgtcttttggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG

Basic information

species Arabidopsis thaliana
transcript AT4G19420.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G35050.1 (Glycine max), 3'ss of exon 2
--gtgagttattaattctgtttatatatttattcattattgttccta-tatagtatatttttgtgtttttttattcttcatctatg-----tcttttggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
    |   | ||   | ||| | |  || |||| | |  ||||| || | || |   || || | ||   | ||  ||    |||      ||      || |||||||||||| ||||| |||||||||||||||||||| ||||| || | |||| | || || || | ||||||| |     |||||
gtaaggaatttttgctgtgtcttttcatatatttaatcatgttcttaatctaatgc-ttattattttcaatgatatttgggatattgaaattcaacatattatgcagTTTGTTTGGATGGGAGTCCACCAGCTTATCATTTTGATAGGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG

upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G35480.3 (Glycine max), 3'ss of exon 2
---gtgagttattaat---tctgtttatatatttatt-cattattgttcctata--tagtatatttttgtgtttttttattcttc-----atctatgtcttttg-gttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
     || || ||  |   ||  || ||||||| ||    || ||  ||  ||   || ||| ||      | ||| || | ||      ||  |  |        ||||||||||||||| ||||| |||||||||||||| ||||| ||||  || | |||| | || || || | ||||||| |     |||||
gttaggaatttttgctgtgtcctttcatatattaatcatcttcttaatctcatgcttattattttcaatgatgtttatactatttgggaaattgaaattcaaaatattttgcagTTTGTTTGGATGGGAGTCCACCAGCTTACCATTTTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG

upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08230.1 (Glycine max), 3'ss of exon 1
gtgagttattaattctgt----ttatata---tttattcattattgttcctatatagtatatttttgtgtttttttattcttcatctatgtcttttg-gttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
|||||  |||  |  |||    | ||  |   || ||||   |||| | |||| |    || | ||    |  | |||  |  ||  | |  |   | ||  |||||||||||| |||||||||||||||||||| || || ||||  || | |||||  || || || |  ||| |  | ||  |||||
gtgagaaatttttgttgtgatatcatggaactttaattctccattgcttctatttttagtaatatttatataatatataataaattgaagcttaacgtgtcatgcagTTTGTTTGGATGGAAGTCCACCAGCTTACCACTTTGATAAGGGATTTGGAAAAGGGATTAACAACTGGATTGTTCACATTGAG

upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G17120.1 (Glycine max), 3'ss of exon 1
--gtgagttattaattctgt--ttatatattt---attcattattgttcctatatagtatatttttgtgtttttttattcttcatctatgtcttttg-gttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
  | || || ||  || ||   |||   |  |   ||||   | || | |||| |     | | ||    |  |  ||  |  ||  | |  |   | ||  |||||||||||| ||||||||||| |||||||| || || ||||  || | |||    || || ||||| ||| |  | ||  |||||
gtgagaattttttgttgtgacattagggaactataattctccagtgcttctatttttagcaatatttatataatagatgatatattgaagcttaacgtgtcatgcagTTTGTTTGGATGGAAGTCCCCCAGCTTACCACTTTGATAAGGGATTTGGGGAAGGTATTAATAGCTGGATTGTTCACATTGAG

upper sequence: AT4G19420.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08240.1 (Glycine max), 3'ss of exon 2
gtgagttattaattctgt----ttatata---tttattcattattgttcctatatagtatatttttgtgtttttttattcttcatctatgtcttttg-gttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
|||||  |||  |  |||    ||||  |   || ||||   |||||| |||| |    || | ||    |  | |||  |  ||  | |  |   | ||  |||||| ||||| |||||||||||||||||||| || || ||||  || | ||||   || ||  | |  ||| |  | ||  |||||
gtgagaaatttttgttgtgatattatggaactttaattctccattgtttctatttttagtaatatttatataatatatgataaattgaagcttaacgtgtcatgcagTATGTTTGGATGGAAGTCCACCAGCTTACCACTTTGATAAGGGATTTGGAGAAGGGATTGACAACTGGATTGTTCACATTGAG

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|116427943|gb|EG470535.1|EG470535
EST:     ACTGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCG                         TTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
genomic: ACTGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCGgtgagttatt ... ggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
EST: gi|124708644|gb|EH800046.1|EH800046
EST:     TGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAGGGGGCCG                         TTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
genomic: TGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCGgtgagttatt ... ggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
EST: gi|116448741|gb|EG491333.1|EG491333
EST:     ACTGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCG                         TTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
genomic: ACTGTTTGTCAATATTACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCGgtgagttatt ... ggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAA
EST: gi|125191744|gb|EL206698.1|EL206698
EST:     TACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCG                         TTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATA
genomic: TACATTTGTTCGAAACGCAGTCGCTAAAGGGGCCGgtgagttatt ... ggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagtatatttttgtgtttttttattcttcatctatgtcttttggttttgcagTTTGTTTAGATGGAAGTCCACCAGCTTATCATTTGGATAGAGGTTCTGGAACTGGAATCAATAGTTGGTTGATACAGCTTGAG
                                       tcttttg  CT-rich tract
      tatatttttgtgtttt  TA-rich tract