Sequence
atgc intronic sequence ATGC exonic sequence...gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
Basic information
species | Glycine max |
transcript | GLYMA05G06110.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 2
-gttgcttgatataaaataa--agttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| | ||| | ||| | | | |||| | | | || | | | | | | || | | | | || | || || | ||| |||| || || | ||| |||| || |||||||| ||||| |||| ||| | ||||||||||||||||| ||||| ||||| ||||| ||||| | || |
cctcaatagatttttaatgacgaataattataaacaggaaatatgttatctcgttcatgcctaataatttctttatggtatc---ctgtatttttatgaacagGAGATAGCAAGTTACTTGGGGCTAGAACTTGGGAAGATAACCATAAAGAGGTTTGCTGATGGTGAAATATATGTTCAGTTGCAAGAAAGTGTACGGGGCT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatt-tgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
|| | | | |||| | | ||| || | ||||| || || ||| | | || | | | || |||| ||||||||||| |||| ||||| ||||| ||||| ||| || ||| ||| ||||||||||||| || |||||||| ||| | |||| |||||||||||||
----------gtagttttctcgagacctttggt-tgtcttttttaatcaagttttcttctggtgaagtatatg----ctaaactcttggaattttgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
--gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| | | || ||| ||| | | | ||| | | || | | | ||| | ||| | | || || | | || |||||||||||| |||||||||| ||| || |||||||| ||| ||| | ||||||||||||||||| ||||| ||||| |||||||||||||||| |
ccttcttcttctttataatttggttc-tttttactgtatgaattttttgttaaaac-acttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 1
gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttt-tctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
|| || ||| | | | || ||| || | | ||| | | | | ||||| | | | | | ||| | || ||||||| || | ||||||||||| |||||||||||||||| ||||||||| |||||||| ||||||||||| |||||| |||| || || || |||||
----------gtagaagaaaagctttcttttgt-tctcgttgtctctattgttaaaactttggctgtttgttcctccctttgtctcttttgttgctatcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 1
gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
| | ||| | || || ||||| ||||| | ||| |||| ||| || ||| | ||||||| || ||||||| || | ||||||||||| |||||||||||||||| ||||||||| |||||||| ||||||||||| |||||| |||| || || || |||||
---gtagaaggaaaactttcttttgttctcattgtctc--tattgttaagactttcgctgttttgttcctccctttgtctcttc-tgttgct---atcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
ttctaac putative branch site (score: 1)
ttgcttt putative PPT
ttttatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
gttgctt
- - - - - - aaaataa
- - - - - - - - - - gttggta
- - - - - - - - - - - - - - -tggtgtc
- - - - - - - - - - - - - - - - - - - - - - gggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgtgtt