Sequence
atgc intronic sequence ATGC exonic sequence...aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaatttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
Basic information
species | Glycine max |
transcript | GLYMA08G24160.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 11
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaat-ttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
|| | || | || || || | | | || | | ||| | || | |||| | | ||||||||||||| ||||||||||| | ||||||| |||||||||| ||| ||||| ||
gtgagaatcatcttccttgggccatttccatggttgtccccatcacaaaacaggttataacttcttagtatcaataacccttgttttcaaagccactgcagAGTAAAAATGGTGGTTTAGCAGTCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 11
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaat-ttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
|| | || | | || || | | || | | | | | ||| || | |||||| | | | |||||||||| |||||||||||||| ||||||| |||||||||| | | ||||| ||
gtgagactcatcttccttatgccatttctatggttatccccttcacaaaataggtcataacttcttagtagcaataacccccattttttaaaccaccgtagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGCAGGAGCTTCAAAATGGTTGGAG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 8
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaatttacctttaactaaaaacattttgtttg---ttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
|| | || | | || || || | ||| || | || || | | | | || | | |||| | | |||||||||| |||||||||||||| ||||||| || ||||||| ||| ||||| ||
gtgagaatcatcttccttacgccatttccatggttgtgtccccattgtaaaataggtcataacttcttatgagcaataatccccatttttgaaaccactatagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGTAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 11
---------aagaagttggggttgtacaaaggactttga---ttagtgatgctttat--ttacttttactaccaaattt---acctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
| || | || | ||| | | || || | | || | | |||||| | | ||| ||| | ||| | |||||| ||||||||||||||| ||||||||||| || ||||||| |||||||||| ||| ||||| ||
gtgagaattatcttcttacgcttttcaaaacagcatggaacctttcttgtatttggtgatgactttttcaaaagtttttcttaccatcaacaacccccattttccaaaccattgcagAGTAAAAATGGTGGTTTAGCAGCTTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 4
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaat-ttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
|| | || | || || | | | | || | | ||| | || | |||| | ||||||||||||||| ||||||||||| | ||||||| |||||||||| ||| ||||| ||
gtgagaatcatcttccttgggccatttccatggttttccccatcacaaaacaggttataacttcttagtatcaataacccttgttttcaaagccattgcagAGTAAAAATGGTGGTTTAGCAGTCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 9
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaat-ttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
|| | || | | | || || || | | | | | | | ||| || | |||||| | | || |||||||||| |||||||||||||| ||||||| |||||||||| ||| ||||| ||
gtgagaatcatcttccttacaccatttccatggttgtccccatcacaaaataggtcataacttcttagtagcaataacccccattttttaaaccactgtagAGTAAAAATGGTGGTTTAGCTGCCTGGGAGCCTGCAGGAGCTTCAGAATGGTTGGAGMapped 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|209716122|gb|BW662320.1|BW662320EST: TGGAACCTGAAAGGTTGTACGATTCAGTCAATGTCTTGTTGTCGCTTCAG AGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGG
genomic: TGGAACCTGAAAGGTTGTACGATTCAGTCAATGTCTTGTTGTCGCTTCAGgcaagtacca ... gttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacttttactaccaaatttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
aactaaa putative branch site (score: 2)
tttaactaaaaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaagttggggttgtacaaaggactttgattagtgatgctttatttacttttactaccaaatttacctttaactaaaaacattttgtttgttattgcagAGTAAAAAAGGTGGTTTAGCTGCATGGGAGCTTGCAGGAGCTCAAGAGTGGTTAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - ggggttg
- - - - - - - - - - - gactttg
- - - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca