Sequence
atgc intronic sequence ATGC exonic sequence...aaataattatctgtatgtgcttattcttagaattttattttatttcttgtgttcactaaatttatgaagtagttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
Basic information
species | Glycine max |
transcript | GLYMA08G34030.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 6
----aaataattatctgtatgtgcttattct-tagaa--ttttattttatttcttgt-gttcactaaatttatgaagtagttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
||||||| || | | | || |||| ||||| ||| | ||| | | ||| ||| ||||| || | | | ||| || | | || | | || || || |||||||| || || ||||| || || || | ||| |||||||||||||||||||||||||| ||||| ||||| || || | ||||
agaaaaataatgatttcttgcagttttttctgtagaaatctttgtggcattattaatagtttgcta--tttattaattgatgc--ctgttactgtgtcctgcagTCC-TCTAGCCGTTTTGATGAACTACCAGATGAATTAGATCCCATTGGGAAACTTCCAGGATCATTTGATGATGGGGATCCACAAACCACGAACTTATATG---
upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 6
aaataattatctgtatgtgctta-ttcttagaattttattttatttcttgtgttcactaaatttatgaagtagttctactgatagttt---tccccttaaacagTCC---AGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
| | || | | || | || | || | || || || | | | | | || || | || | |||| | | || |||||| || || |||||||| || || ||||| ||||| || | ||| | | |||||||||||||||||||||||||||||||||| || || | ||||
-actgatgtccagctaatgagaaatttgtgtgatcattttgtagtttctatatgaatt---ttaatagttttttttcattgatgcctaacattattttgtgcagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG---
upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 6
aaataattatctgtatgtgcttattcttagaattttattttatttcttgtgttcactaaatttatgaagtagttctactgatagttt---tccccttaaacagTCC---AGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
|| | || | | || | | | | | ||||| | || | | | || |||| | | || | |||| || | || |||||| || || |||||||| || || ||||| ||||| || | ||| | | |||||||||||||||||||||||||||||||||| || || | ||||
aactgatgtccagctaatgagaaatttgtgtgatc-attttgtagtttctat--atgaattttaatagtttctttcattgatgcttaaaattattttgtgcagTCCTCGAGCCGGTTTGATGAACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATG---
upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 5
aaataattatctgtatgtgcttattcttagaattttattttatttcttgtgttcactaaatttatgaagtag--------ttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
| ||| ||| | |||| || | | || | ||||| || | ||| | | | | || || | | | ||| | | | | | || | |||||||||||||||||||||||||| || |||||||| ||||| ||||||||||||||||||||||| |||||||| ||||| ||||
-----agtatgcatatatagttatgtttctgttgtctttctgcatcttgcatttgtgatgtttgtacatttgagtatactttttaataaggttattctttctcagCTGCCTAGCAGATTTGATGAGCTGCCTGATGACTTTGATCCGAGTGGAAAGCTTCCTGGATCATTTGATGATGGTGATCCACAAACTACTAATCTCTATG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtgttcactaaatttatgaagtagttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
tactgat putative branch site (score: 2)
ttttcccctt putative PPT
taaatttatgaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaataattatctgtatgtgcttattcttagaattttattttatttcttgtgttcactaaatttatgaagtagttctactgatagttttccccttaaacagTCCAGTCGCTTTGATGAGCTGCCTGATGACTTTGACCCAAGTGGAAAACTTCCAGGATCATTTGATGATGGTGATCCTCAAACTACAAATCTTTATGTTG
- - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - -tgttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctactg