Sequence
atgc intronic sequence ATGC exonic sequence...gtctttatatattgtttttcattcacatatgccatgatcagtagtgattttccagagctaagtattttgatccctttctgatgcatctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
Basic information
species | Glycine max |
transcript | GLYMA01G16370.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g10780.1 (Oryza sativa), 3'ss of exon 7
--------------gtctttatatattgtttttcattcacatatgcc--atgatcag----tagtgattttccagagctaagtattttgat---------ccctttctgatgcat--ctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
|||| ||| || | | | || | || ||||| | || || |||| | | ||| || || || | | ||||| | || ||||||||||||||||||||||| ||||| || |||||||| |||||||| ||||| || ||||| | || || || ||||| ||||
gtttgaatacaatcaccttttccctttgagttgaggcaaggtttacctcagaattgagatttagtggaagtttgaagtaaatggttttagcagtacaaaatgttaacatatgtatgtcttgtattatacagGAATTGCTTCAAATGTTTGGCTTGCCATATATAATTGCACCTATGGAAGCTGAAGCTCAGTGTGCATACATGGAAATGACTAACCTTGTCGATGGAGTTG
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------------------------gtctttata-tattgtttttcattcacatatgccatgatcagtagtgattttccagagctaagtatttt--------gatccctttctgatgcatctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
| || | | || | | | | ||| | | | | || || | | |||| | || || ||||||||| | | || |||| | || ||||||||||| ||||||||||||||||| ||||||||||| |||||||||||||| || ||||| | | || || |||||||| ||||
gtttgaagtgattcttgattgcttattttgaactgaataatttaaggttcttgatgcaaagttatatcataatttgtgcattgaaaatagagatataagtaaacaacttggtttagtaataaagaaacactaaccaaaagtcccattgatgacaaatgccactctgatgcagttc-catgttgcagGAGTTGCTCCAAATGTTTGGGTTGCCATATATTATTGCACCAATGGAAGCTGAAGCTCAATGTGCATACATGGAAATAAATAACCTCGTTGATGGAGTTG
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0066g01630.t01 (Vitis vinifera), 3'ss of exon 8
--gtctttatatattgtttttcattcacatatgccatgatcagtagtgattttccagagctaagtattttgatccctttctgatgcatctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
| || || | | || ||| || || || | | | | | | ||| | ||| || | | | ||||| | | || ||||||| || |||||||||||||| |||||||||||||| || |||||||| |||||||||||||||||| ||||||||| || || |||||||| ||||
aaatgttgatctgtatttcttcttttctat-tgataaatttcattcttctaaaagaaagccatctatatttaatgcat-ctgattttcttttttgattgcagGAACTTCTCCAAATGTTTGGCTTACCATATATTATTGCACCTATGGAAGCTGAAGCTCAATGTGCTTATATGGAACTTGCAAACCTTGTTGATGGAGTTG
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S31_24V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------gtctttatatattgtttttcattcaca----tatgccatga-tcagtagtgattttccagagctaagt-attttgatccctttctgatg-catctg-atactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
| || ||| || | | | | | | |||| || | || | | | | || | || | | | | || ||| | || | || |||| || ||||||||||||| ||||| ||| | |||||||| |||||||||||||| |||||||| | | | || ||||| ||||||||||||| |
gtaagtaatgaccgctaaaattttccaagggttcgggtatgattaatgagtgaaaatactttgcctcgaattagaactaggtccttaactcttgcttgttgccacacaagtgtagtgacatttatgtattgtgcagGAGCTGTTGCAAATGTTTGGGTTGCCTTATGTGATTGCTCCCATGGAAGCAGAAGCACAATGTGCGTTTCTAGATGCAGAGAAGTTAGTTGATGGTGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattttccagagctaagtattttgatccctttctgatgcatctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
taagtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttatatattgtttttcattcacatatgccatgatcagtagtgattttccagagctaagtattttgatccctttctgatgcatctgatactctgtagGAACTACTGCAAATGTTTGGCTTGCCATATATTATTGCTCCAATGGAAGCAGAAGCTCAATGTGCTTATTTGGAACTTGAGAAACTAGTTGATGGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - -cattcac
- - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcat