Sequence
atgc intronic sequence ATGC exonic sequencegtatatgtcttatgcgatgaatatctgatagttgttctgctatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
Basic information
species | Glycine max |
transcript | GLYMA13G38980.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 10
------gtatatgtcttatgcgatgaatatctgata-gttgttctgctatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
|| | | | ||| || | ||| || | | ||| || | | | | | |||| |||||||| |||||||||||||||||||| || ||||| || ||||||
gtaatagtttcttacatataaagagatgcttaaatatattaatattagatgcctcttttaactggtgtctttgcagGATGTTGTATGTATGAGATGGCTGCTCATCGACCTGCTTTCAAGGCTTTT
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatatgt---cttatgcgatg-aatatctgatagttgttctgctatgg--ctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
|||| ||| | | | | || || | | | | || | | | || |||| | || || |||| ||||||||||||||||||||||| |||| || ||||| |||||||||
gtatgtgtaaccctgtcctttgtaaagtttaagatttttgttattgtgaaactaagcctgtatgctggtgaacagGCTGTTGTATATATGAGATGGCTGCGTATCGACCTGCTTTCAAAGCTTTT
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
gtatatgtcttatgcgatgaatatctgatagttgt---tctgc-------tatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
|||| ||| || || | ||||| || | ||||| | |||||||| | | || | || |||||||| ||||| ||||||||||||||||||||||| || ||||| ||||||
gtatgtgtttt-catagtgtctgg-tgatatttatggatctgcagttgtttgtggctaaattttgcatt-gctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgatgaatatctgatagttgttctgctatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
ggctaaa putative branch site (score: 3)
tttttgtt putative PPT
taaaatgtatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgtcttatgcgatgaatatctgatagttgttctgctatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT