Sequence
atgc intronic sequence ATGC exonic sequence...ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacattttttttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
Basic information
species | Glycine max |
transcript | GLYMA07G00330.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 11
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacatttttt---ttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
| | || | || | || || ||| | | | || | | | | | | ||| | |||| | ||||||||||||| ||||||||||||| |||||||||||||||||| ||| ||||| ||
gtgagaa--tcatcttccttgggccatttccatggttgtccccatcacaaaacaggttataacttcttagtatcaataacccttgttttcaaagccactgcagAGTAAAAATGGTGGTTTAGCAGTCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 11
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacatttttt---ttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
| | || | | || || || | || | | | | | | | | ||| | |||||||| | | |||||||||| ||||||||||| || |||||||||||||||||| | | ||||| ||
--gtgagactcatcttccttatgccatttctatggttatccccttcacaaaataggtcataacttcttagtagcaataacccccattttttaaaccaccgtagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGCAGGAGCTTCAAAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 8
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaac--taaacaacatttttt---ttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
| | || | || | | || || ||| | ||| || | || || || | | | ||| | ||||||| | | |||||||||| ||||||||||| || |||||||||| ||||||| ||| ||||| ||
gtgagaa--tcatcttccttacgccatttccatggttgtgtccccattgtaaaataggtcataacttcttatgagcaataatccccatttttgaaaccactatagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGTAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 11
------ataataagttagggttgtacaaaggactttg--atcattgatgc-tttatttacttttactaccaaatttatttttaac-taaacaacatttttttt-------attgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
|| || | | | | |||| | || | | || || ||| | | | | | ||| || || ||| | | |||||| |||| ||||||||||||||| |||||||||||||| |||||||||||||||||| ||| ||||| ||
gtgagaattatcttcttacgcttttcaaaacagcatggaacctttcttgtatttggtgatgactttttcaaaagtttttcttaccatcaacaacccccattttccaaaccattgcagAGTAAAAATGGTGGTTTAGCAGCTTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 4
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacatttttt---ttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
| || | | || || ||| | | | || | | | | | | ||| | |||| | ||||||||||||| |||||||||||| |||||||||||||||||| ||| ||||| ||
---gtgagaatcatcttccttgggccattccatggttgtccccatcacaaaacaggttataacttcttagtatcaataacccttgttttcaaaaccactgcagAGTAAAAATGGTGGTTTAGCAATCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 4
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttat---ttttaacta--aacaacatttttttt-------attgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
|| || | | ||| | |||| | || | | || | | |||| || | | || || ||| || |||| ||||||||||||||| ||||||||||||| |||||||||||||||||| ||| ||||| ||
-------gtgagaatcatct----tccttgggccatttccatggttttccccatcacaaaacaggttataacttcttagtatcaataacccttgttttcaaagccattgcagAGTAAAAATGGTGGTTTAGCAGTCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 9
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacatttttt---ttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
| | || | || | | | || || ||| | | | | | | | | | | ||| | |||||||| | || |||||||||| ||||||||||| || |||||||||||||||||| ||| ||||| ||
gtgagaa--tcatcttccttacaccatttccatggttgtccccatcacaaaataggtcataacttcttagtagcaataacccccattttttaaaccactgtagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAGMapped 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|10238321|gb|BE807137.1|BE807137EST: GGAACGCTGAAAGATTATACGATTCAGTCAATGTCTTGTTGTCGCTTCAG AGTAAAAAAGGTGGTTTAGCACCATGGGAGCCTGCAGGAGCTCAAGAGTGG
genomic: GGAAC-CTGAAAGATTATACGATTCAGTCAATGTCTTGTTGTCGCTTCAGgcaagtacca ... tttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttacttttactaccaaatttatttttaactaaacaacattttttttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
aactaaa putative branch site (score: 2)
ttttttttatt putative PPT
taccaaatttattttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataataagttagggttgtacaaaggactttgatcattgatgctttatttacttttactaccaaatttatttttaactaaacaacattttttttattgcagAGTAAAAAAGGTGGTTTAGCAGCATGGGAGCCTGCAGGAGCTCAAGAGTGGTTAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - -gggttgt
- - - - - - - - - - - - gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaca