Sequence
atgc intronic sequence ATGC exonic sequence...aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
Basic information
species | Glycine max |
transcript | GLYMA09G10390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgat----atagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
||| | | | ||| | | | || | | |||| || | ||| || |||| | || || | |||| || |||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||| |
---aatgttggtaatacttttagagcttgctttgattt-tgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgata--tagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| | || || | | | ||| || | | || ||||| | || | || | | | | | | || | | || | ||||||| || |||||||||||||| ||| | || |||||||| |||||||||||||| ||||| | || || ||||| || ||||| |||||||||||
gatgatgtatagcatatccaccaag--aaccaccatataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G432083_T01 (Zea mays), 3'ss of exon 3
aaagcagtttattaaaaaaaagaagcaaatcctaacatgc-attaagtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
|| | | | ||| | | | | | | | | | | || || | | | || | || ||| || |||||||| || || || ||||| ||||||||||| ||||||||||||||||||||||| || || ||||||| ||||| || ||||| || || ||| |
-tcttgattcaatgctgggacaaagtactttttgttgttctagtgttcaaccaaaacaaactaacgccaacaaactgacttgcatgttgaatgacctatagGGTGGTGGGCCATATTATCTTATAGGCCGTGCACTTGGTCCTGAAGTTGGAGTTAGTATAGGATTATGCTTCTTCCTCGGGAATGCAGTGGCTGGATCCA
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
-----aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| | | || || | | || |||| | || | ||||||| || | | || | | || | | |||| ||||||||||| || || |||||||| || |||||||||||||| |||||||||||||||||||| ||||| || ||||| || ||||| || || ||| | |
ctttcataactcttgttttactggcttaggc--ttccttctttttgttgtcctttttgtattaattgatacca--atctattttcttgacatctttgtttc-tagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------aaagcagttta--ttaaaaaaaa-gaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattt---tcttgtgt-atgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| |||||| | | || | | | | ||| | || ||| || | | | | | ||| ||| | | | ||| || || |||||||||| || |||||||| ||||| || || ||||||||||| ||||| || || || || || || || ||||||||||| |||||||| |||||
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S139_48V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------aaagcagtttattaaaaaaaagaagcaaatcctaacatgca--ttaagtaggct-ctattaataaatgatatagtttagtatt---ttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
|| ||| || | || || ||| | || | || || | | ||||| || | || | || || || ||| | | | |||||||||| |||||||| || ||||| || || ||||||||||| ||||| || || |||||||| || || ||||| ||||| ||||| || | |||
gtttgttgtcgtttcctaagcatttacgaattaacacgcttgattgagactgtattttatagtggaagtggttgatctaataatacacaatgcatttgaggtcaataatattgcacttactgcctggccacttgctcacattgctatttggaaggaagttacatcagaatggaattaatgtttccttaattcagGGTGGGGGTCCTTACTACCTGATAGGACGGGCACTTGGTCCTGAGGTTGGTGTGAGTATTGGTCTCTGTTTCTTCCTTGGAAACGCTGTGGCTGCCGCAA
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S14_51V6.1 (Physcomitrella patens), 3'ss of exon 5
aaagcagtttattaaaaaaaa-gaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtat--tttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| || | || | | | || | | | || || || | | | || | |||||| | || || || ||||||| || ||||||||||| |||||| | || || |||||||| ||||| || |||||||| || |||||||| || || |||||||| || ||| |
--tgtggtctgtttatggtgttgtaacatggctcatgaagctttgtttaaagtttga-atccaaaatttcagtttaaaacaacgcattctgctacggttgcagGGTGGAGGTCCTTACTATCTGATAGGCAGGGCGCTGGGTCCTGAGGTTGGGGTCAGCATTGGACTTTGCTTTTTTCTCGGCAATGCTGTGGCTGGATCTT
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23975 (Selaginella moellendorffii), 3'ss of exon 3
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgta-tgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| ||| || | ||||| ||| || | | || | | |||||||| ||||| || ||||| || || || || |||||||| ||||| || |||| ||||| || ||||||||||| |||||||| ||||| ||| |||
-----------------------------------------------gttcaaaattttgcgttgcgacagtttttcttttggttaagcactggtttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC
upper sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21598 (Selaginella moellendorffii), 3'ss of exon 3
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgta-tgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| ||| || | ||||| ||| || | | || | | |||||||| ||||| || ||||| || || || || |||||||| ||||| || |||| ||||| || ||||||||||| |||||||| ||||| ||| |||
-----------------------------------------------gttcgaaattttgcgttgcgacagtttttcttttggttaagcactgctttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCACMapped 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|208140500|gb|GD938650.1|GD938650EST: TCCTTACTTCAATATCATTGAGTGCTATTGCAACCAATGGAGCCATGAAG GGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGA
genomic: TCCTTACTTCAATATCATTGAGTGCTATTGCAACCAATGGAGCCATGAAGgtatgcattg ... tgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
tattaat putative branch site (score: 2)
tctattaataaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgatatagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - -aaaaaaa
- - - - - - - - - - - - -caaatcc
- - - - - - - - - - - - - - - - - acatgca