Sequence
atgc intronic sequence ATGC exonic sequence...tcactagaaatccatgaagtgctcctcatagcgcaatgtgtagtgcttactccttatatcggtagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
Basic information
species | Glycine max |
transcript | GLYMA03G03120.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 14
---------tcactagaaatccatgaag-tgctcctcatagcgcaatgtgtagtgcttactccttatatcggtagctttgt-atcctaggtt-atactatgtatttt--------tacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
|| | ||||| | || || | | | | ||| || || || | | || | || || | | || || | | | ||| || |||| ||| ||||||||||||||||||| | | | ||||| || |||||||||||||| |||| ||||| || ||||||| ||
gtatttacacagttaacccttcatgatgatgttctttacatggttttgt-tacgctttgctgttgacatgaattactgaaagatgccaaattcatcttctttgtttcctttataatatagGTCATGCTTGATTTTCAAGCAGCTGAGAGGCAAAGACTTGAGGAACCAGCTTCTGATGTTGGCTTGGAATCTCTATGTGCATTG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 10
---------------tcactagaaatc-catgaa-gtgc---tcctcatagcgcaatgtgtagtgctt---actccttatatcggtagctttgtatcctagg----ttatactatgtatt-tttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
|| ||||| | ||| || || | | ||||| |||| ||| | ||| || ||||| ||| |||| ||| | | ||| ||||| ||| ||||||||||||||||||| | | | || || || || ||||||||||| ||||||||||| || ||||||| ||
gtatttatatagttaccatatgaaattacgtgactatgtgagtctactgggtttgttgtgttacgcttcacacttttgtaatcagttaatttgttatttagatgttttattttatttgtcatttgcagGTCATGCTTGATTTTCAAGCAGCTGAGAGGCAAAGGCTTGAGGAGCCAGCTTCTGATGTTGGTCTGGAATCTCTATGTGCATTG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 16
-tcactagaaatccatgaagtgctcctcatagcgcaatgtgtagtgcttactccttatatcggtagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
| || | | | | | | | || | ||| || | | | | || | | ||| | || ||| | ||||| ||||||||||| ||||||||||||||||||||| | || ||||| || ||||| ||||||||||||||| |||| ||||||
ccctctttcattgtgtctaac-ttttatacttcttaaatttcgtaacttttgtagcattgtgcatgttctaaattttgattcatattgtgaattacttcagGTTATGATTGATTTCCAAGCAGCTGAAAAGAAGAGAGTTGATGAACCTGCATCTGATATTGGTCTGGAACCTCTATGCGCTATG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 15
tcactagaaatccatgaagtgctcctcatagcg-caatgtgtagtgcttactccttatatcggt-agctttgtatcctaggtt---atactatgtat-ttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
||| || | | || ||||| | | | | | || || || | | | | | || | ||| || | | || |||| |||| ||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||| |||||||||| |||
------taaaccccttttttacttctcattgtggttgtctatcatggtttgtcaatgtcctatttaaaatcataattgatgttcagattcacttcatgttttttagGTAATGATTGATTTTCAAGCAGCTGAAAAGCGAAGACTTGAAGAACCTGCTTCTGAAATTGGTCTGGAATCTTTATGTGCAATG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 15
tcactagaaatccatgaagtgctcctcatagcg------caatgtgtagtgcttactccttatatcgg-tagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
| || | | || ||||| | | | || || | | ||| | | | | || | || | ||| || ||||| |||| ||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||| |||||||||| |||
------aaccccctttttttacttctcattgtggttgtctatcatggtttgtcaatgtcctatttaaaatcacaattgatgttcggattcacttcgtgttttt-tagGTAATGATTGATTTTCAAGCAGCTGAAAAGCGAAGACTTGAAGAACCTGCTTCTGAAATTGGTCTGGAATCTTTATGTGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttactccttatatcggtagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
tgcttac putative branch site (score: 2)
tattttt putative PPT
ttatactatgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactagaaatccatgaagtgctcctcatagcgcaatgtgtagtgcttactccttatatcggtagctttgtatcctaggttatactatgtatttttacagGTGATGATTGATTTTCAAGCAGCTGAAAAGAAGAGACTAGAAGAACCAGCTTCTGAAATTGGTCTGGAACCTTTATGTGCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - -ccatgaa
- - - - - - - - - -tgctcct
- - - - - - - - - - - - - - - -cgcaatg
- - - - - - - - - - - - - - - - - - - tgtagtg