Sequence
atgc intronic sequence ATGC exonic sequencegttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
Basic information
species | Glycine max |
transcript | GLYMA07G38510.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| ||| || || | ||| | || || | |||| | || | |||| | || |||| ||| | ||| | || ||||||||| |||||||||||||| || |||||||||||||| ||||||||||| || || || || || ||||| || || ||||| ||||| |||||||
-----------------------------------agtagcctgatatgactgctccat--ctcattattcaatatattttgttatactagaattttactgatatgacagctgtctttcattatttgttta---ctgcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggttt--gtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | || | | ||| | || | ||| || | | | ||| ||| || || | || ||||| | |||| || | ||| | ||||||||||||||| |||||||| || ||||||||||| || || |||||||| || || || || || ||||| ||||| ||||| || || ||||| |
---------------------------------ctgtactcagtgttctatgtttgtgtgattcctattt-atcagtccatcctatttgtgactctaat-----tcctgactgatgc---atcttttgatagctttttgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATCTTGGCGAATGCTGATTGTAAGCTCAAAATATGTGATTTCGGCCTTGCAAGGGTAGCTTTTAG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttag--attcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtt--tgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| ||| ||| ||||||| || |||| ||| | || || || | | ||||| | || ||||| | ||| ||| | || || ||||||||||||||| |||||||| || |||||||||||| | ||||||||||| || || || || || |||||||| || | || ||||| ||||||||
---------------------------tcattactaggggctcctaatctgtctgtttc-----cgctgtgtccttttagtggc---------actaacatgcctgatatgactgatgc---atctttcaatagcttattgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 1
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtt--tgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | | || | || ||| ||| | ||| | ||| | | | ||||| | || ||||| | ||| ||| | || || |||||||||||| || |||||||| || |||||||||||| | ||||||||||| || || || || || ||||| || || || || ||||| |||||||
--------------------------------taggggcttctcttcttactgttttccagtga--gttctgttagtggcagtggc-----actaacatgcctgatatgactgatgc---atctttcaatagcttattgcagCAAATGTATTCCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTAGCAAGAGTAGCTTTCAG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| |||| | | || ||| ||| | ||| | | || | | || | |||| ||||| || ||| ||||| ||||| || ||||| || || ||||| || || ||||||||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||
--------------------------------------------gttaagctagcgagcaat-aaaatttcattgattagtataagtttatgattat---ctttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gttatgatctttatatttag--ctagt---ttttatt----tttagattcctaatgcagctttt-tcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgatttta----aactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| | | ||| | | ||| |||||| | || | || ||||| | | | |||||||| | ||| | | || | | |||||||| | | |||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
| | ||| || | || || |||| || || ||| || || || ||| | || || || ||| || | |||| ||||||||||| || ||||| |||||||| ||| | || ||||| ||||| ||||| ||||| |||||||| || || ||||| | ||||||||||
----------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaa-tgaatgtgtgtctcgtttggatgttgacg-tgcttcta----tttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaa---tgggtttgt--agCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
|| || | | || | | || | | | || ||| || | || || | | ||| || | | || | |||| |||| ||| ||||| ||||| || || || |||||||| || | || ||||| |||||||| |||||||| ||||||||||| || ||||| ||||||| || |
--------------------------------------------tcacaactctcactgtacaaaagactgatgggatgtggtcctttttggatttc-tgtctgtttttgtggatgttgacgtcttcatgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA