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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattaaaagccttttaagtagatcaaaagtttgctcatgtgtgtgtgtgtgtgaaagatgtacaatttgatcttagtgttaaattatcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG

Basic information

species Glycine max
transcript GLYMA01G02850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
gtaa-gtattaaaagccttttaagtagatcaaaagtttgctcatgtgtgtgtgtgtgtgaaagatgtacaatttgatcttagtgttaaattatc-ttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG
||||   | |         || |    || | |  |    | |  |   || |  |      ||  |   |||  |||  | | ||   ||    || | |||||||||||||| ||||||||||| || || ||||||||  |||| ||||||||| | |||||| | |||||||| |||  |||  ||||
gtaacacacttcttatgcattgatgctatgatatataacttaacataactg-gcatccttgggactttagatt--atccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG

upper sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G057037_T01 (Zea mays), 3'ss of exon 4
gtaag-tattaaaagccttttaagta-gatcaaaagtttgctcatgtgtgtgtgtgtgtgaaagatgtacaatttgatcttagtgttaaattatcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG
||| | | ||  ||    | | |||| |||   | |     | |  |   | | | | |  | | | || |  |||  |  | | || | |    || ||||||||||||||||  |||| ||||||||||| || ||||||||||| ||||||||| | |||||| | || ||||| |||   ||||||||
gtatgctcttctaattactattagtatgattttaggaca--tgagatagctttctttatccaggctttaga--ttggcca-actctttattccaattctgtagATATGTGATGCCATTGCAGTTGCAAAGATTCTTAATGCTACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG

upper sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gtaagtattaaaagccttttaagtagatcaaa--agtttgctcatgtgtgt---gtgtgtgtgaaagatgtacaatttg----atcttagtg-------------ttaaattatcttgt--gtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG
                                |   |||||||||  |      | |  ||||   |  || | || |  ||    | | | ||  | ||||    |||     ||||| ||              |||| || | ||||  |||||| |||||||| ||||||||||| |||||| | |||||||| || ||||||||| | |||||| |||||||||| ||||| ||||| ||
gtaggtaattctaggtttgccactacattctatggatattaaaagggtcaaggatggcccaaacaggaatgattatctcggttaaatttttatgtcacatgtttgctttagaaaatcttggttggttgttcatatcttaatttgtattgtttgtagATTTGTGATGCTGTTGCTGTTGCTAAGATATTAAATGCTACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG

upper sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S215_43V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------gtaagtattaaaa---gccttttaagtagatcaaaagtttgctcatgtgtgtgtg-tgtgtgaaagatgtacaatttgatcttagtgttaa-attatcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG
                           |   | ||||||   ||  |||   | | |   ||   |  | |||  | |  | ||         ||||    ||| ||      ||   || |||||| | |||| |||||||| |||||||||||||| || |||||||| ||||| ||  | ||  |  | ||  | ||||| || |||  ||| || ||
gtcagacttccttctaacagattttcttggattttaaaacttgctgtttgtctcgttggcaatgctattgatgattattagatgccattttattgtatgtgttggtcaactcattcgtataatcttg-gcagATTTGTGATGCGGTTGCTGTTGCAAAAATTCTGAATGCAACTCTTGTTCTTCCTCATTTCGATGTTAATCCAGTTTGGAAAGACTCCAG

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|208240145|gb|GE042297.1|GE042297
EST:     GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGG                         ATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
genomic: GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGGgtaagtatta ... tcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
EST: gi|7147128|gb|AW509050.1|AW509050
EST:     GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGG                         ATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
genomic: GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGGgtaagtatta ... tcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
EST: gi|26043675|gb|CA782127.1|CA782127
EST:     GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGG                         ATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
genomic: GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGGgtaagtatta ... tcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
EST: gi|7147562|gb|AW509484.1|AW509484
EST:     GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGG                         ATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC
genomic: GATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAAGATGGGGgtaagtatta ... tcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtgtgtgaaagatgtacaatttgatcttagtgttaaattatcttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG
                       atttgat  putative branch site (score: 5)
                                          ttatctt  putative PPT
                               ttagtgttaaattat  TA-rich tract