Sequence
atgc intronic sequence ATGC exonic sequence...cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
Basic information
species | Glycine max |
transcript | GLYMA08G07780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 3
cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagt-tgtcattctgctccttactttttgaggc--aacattat----------gcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
|| || || || ||||||| | || || | ||| | || | | | ||||| | || || | || ||||| ||||||||||||| |||||| |||| |||||||| ||||| |||| | | ||||| ||| | |||||||| ||| |||| ||||| ||||| || ||||| |||
----------tttttatctg--ttggctcatgtgtgatt-ttggttataaagtccatgttgttttattctacaatttgaacttgaatatcaaatattataatttaatttgcagGATATCTGTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAA
upper sequence: GLYMA08G07780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 4
------cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
|| || | | || | | | | | |||| || | | || | | || | | |||| | | |||||| |||||||| ||| | |||||||||| ||| || |||| ||||||||||||||||| || |||||||| ||||||||||| ||||| |||
ctttaaaggggcttctccttcagtttttccctcctaggaaatagctgtccaaaacaaccgattaatttttctaatgagcaaatttctttgtg------ctgcacagGATCTCTGTAACATTTGTGAACAAGGATGGCACAGAGCAGACAATCAGTGTCCCTGTTGGAATGTCCATCTTAGAAGCTGCTCATGAAAATGACATCGAA
upper sequence: GLYMA08G07780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G013607_T02 (Zea mays), 3'ss of exon 4
cacaactact--attgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttg-tcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
| |||| ||||| || | | | | || ||| | || | || | ||| | ||| |||| | | | ||| || || ||||| ||| | |||||||||| || ||| || || || ||||||||||| ||||||||||| ||||||||||||||||| ||
-agttttactgaattgt-tagtgttgagctttcaataattatttagggtagaagcagtcctctgatgattgttgaggttatttttctccatactgtga-acagAATCTCGGTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAG
upper sequence: GLYMA08G07780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttgtcattctgctccttactttttg-aggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
|| || | | | || || || | || | | | ||| | || | | || | ||| || | ||| |||||||||||||| | ||| |||| |||||||| ||||| | || || | ||||| |||||||||||||||||||||| ||||||||||| || || |||
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgta-gattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaatgcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
tccttac putative branch site (score: 2)
ttacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacaactactattgtaccttgcttatatcatgtgagtttattaaaaaaaaaatgcacagttgtcattctgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGACAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCAGCTCATGAAAACGACATTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- caactac
- - - - - - - - ccttgct
- - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - aatgcac