Sequence
atgc intronic sequence ATGC exonic sequencegttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
Basic information
species | Glycine max |
transcript | GLYMA17G02220.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| ||| | || | ||| | || || | |||| | || | ||| | || |||| ||| | ||| | || ||||||||| |||||||||||||| || |||||||||||||| ||||||||||| || || || || || ||||| || || ||||| ||||| |||||||
-----------------------------------agtagcctgatatgactgctccat--ctcattattcaatatattttgttatactagaattttactgatatgacagctgtctttcattatttgttta---ctgcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 2
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggttt--gtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | | || | ||| | ||| | || | ||| || | | | ||| | | || || | || ||||| | |||| || | ||| | ||||||||| ||||| |||||||| || ||||||||||| || || |||||||| || || || || || ||||| ||||| ||||| || || ||||| |
---------------------------ctgtactcagtgttctatg------tttgtgtgattcctattt-atcagtccatcctatttgtgactctaat-----tcctgactgatgc---atcttttgatagctttttgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATCTTGGCGAATGCTGATTGTAAGCTCAAAATATGTGATTTCGGCCTTGCAAGGGTAGCTTTTAG
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2
gttatgatcactatatttagctagtttttatttttag--attcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtt--tgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| ||| ||| |||||| || |||| ||| | || || || | | ||||| | || ||||| | ||| ||| | || || ||||||||| ||||| |||||||| || |||||||||||| | ||||||||||| || || || || || |||||||| || | || ||||| ||||||||
---------------------------tcattactaggggctcctaatctgtctgtttc-----cgctgtgtccttttagtggc---------actaacatgcctgatatgactgatgc---atctttcaatagcttattgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 1
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtt--tgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | | || || ||| ||| | ||| | ||| | | | | ||||| | || ||||| | ||| ||| | || || ||||||||| || || |||||||| || |||||||||||| | ||||||||||| || || || || || ||||| || || || || ||||| |||||||
--------------------------------taggggcttctcttcttactgttttccagtga--gttctgttagtggcagtggc-----actaacatgcctgatatgactgatgc---atctttcaatagcttattgcagCAAATGTATTCCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTAGCAAGAGTAGCTTTCAG
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | | | ||| ||| ||| ||| | | || | | || | |||| ||||| || ||| ||||| ||||| || ||||| || || ||||| || || ||||||||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||
---------------------------------------------gttaagctagcgagcaataaaatttcattgattagtataagtttatgattat---ctttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
------------------gttatgatcactatatttagc--tagtttt---tatttttagattcctaaggcagctttttca-------tagttaatgtt--ttattataagagctaattattaaatcacatgatcattgtgg--ctgatttta----aactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| | | | ||| || | |||| || ||| | | ||||| | || | |||| | |||| | || | | | | | ||| || |||||||| | | |||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatat-tcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
upper sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaa---tgggtttgt--agCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| || | | || | | || | | | | || || || | || || | | ||| || | | || | |||| |||| ||| ||||| ||||| || || || |||||||| || | || ||||| |||||||| |||||||| ||||||||||| || ||||| ||||||| || |
--------------------------------------------tcacaactctcactgtacaaaagactgatgggatgtggtcctttttggatttc-tgtctgtttttgtggatgttgacgtcttcatgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
ttttaat putative branch site (score: 3)
tgattttaaacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatgatcactatatttagctagtttttatttttagattcctaaggcagctttttcatagttaatgttttattataagagctaattattaaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA