Sequence
atgc intronic sequence ATGC exonic sequence...aatcacactatgtctacctaatatagtaggggcagggaaaatcaatgcttgacttttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
Basic information
species | Glycine max |
transcript | GLYMA16G07850.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 12
------aatcacactatgtctacctaatatagtaggggcagggaaaatcaatgcttgacttttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
||| | || | | || || | | || | | | ||| | |||| || | | | || || ||||||||||||||||| || || ||||||||||||||||| || | |||||||||||||||| ||||| ||
attgtagttcagagcattttgtgattcaattataaaattatactatatggtttcctcttgcttcta-acaatgcccctccccttatttgggtgatcta-----cagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
upper sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G346278_T02 (Zea mays), 3'ss of exon 8
aatcacactatgtctacctaatatagtag--gggcagggaaaatcaatgcttgact-tttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
| | | | | || | | | | | |||| | | ||||| | | ||| | | | ||| || | | |||||||||||| ||||| || || |||||||| |||||||| || | |||||||||||||||| | |||||||
taacgtaacacatttaataatttcaattttcaaaaatataaaaatactatatgactatcctcttgtttttgagaaagtttc---tatttcgggtgatccacagATGTGTGGGAGGGCTGGACGTCCACCATTCGATGATACTGGAACAATTATAATCATGACAAGAAAAGAAACG
upper sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0066g00880.t01 (Vitis vinifera), 3'ss of exon 11
aatcacactatgtcta---cctaatatagtagg--ggcagggaaaatcaatgcttgacttttcca-tgtaatgtatatcatttgaggtaaaacat-ttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
||||| ||| || || | | | | | | ||| ||| || || | || |||||| | | | | ||| | ||||||||||| |||||||| || ||||||||||| ||||| || |||| ||||||||||||||| ||||||||
-------ctatgcctagggcccaaagaaaaaaattatcctagtataagcatgtttgttttcctcaatactttgcttatcatgtcattaagtttgtcttaaaatgcagATGTGTGGGAGGGCAGGTCGTCCACCATTTGAGGATACGGGAATGGCTATAATCATGACAAGACGAGAAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgacttttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
gcttgac putative branch site (score: 4)
taatgtatatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcacactatgtctacctaatatagtaggggcagggaaaatcaatgcttgacttttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- -cacacta
- - - - - - - - - - - - -gtagggg
- - - - - - - - - - - - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaac