Sequence
atgc intronic sequence ATGC exonic sequence...caagacaatttggattttggtgtgaacaaaaaggatatgatttggcttttttattttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
Basic information
species | Glycine max |
transcript | GLYMA06G11470.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------caagacaatttgga----ttttggtgtgaacaaaaaggatatgatttggctttttta----ttttatgtc--gcctattagaaattattaa--------tgtttttgcttccc----ctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
| ||||| || | | | ||| | | || | || ||| ||||| ||| || | ||||| || ||||||| || | ||||||| || ||||| ||||||||||| ||||||||||| ||||| | ||| ||||||||||||||||| |||||| | || ||||| || ||||| || || |
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
caagacaatttggattttggtgtgaacaaaaagg-atatgatttggcttttttattttat----gtcgcctattagaaattattaatgtttttgcttcccct--cagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
| || | |||| | | | | |||| || | ||| ||| | || || || | || | | | | | | ||||| |||||||| ||||||||||| |||||||| || ||||| | ||| |||||||| |||||||| ||||| | || ||||| || ||||| || ||||
---ggagatattaattt----gcaacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA
upper sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------caagacaatttggattttggtgtgaacaaaaaggat----atgatttggctttttt--------attttatgtcg--cctattagaaattatt--aatgtttttgcttccc--ctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
| |||| | || || | | | | | | | || |||| | ||| || || | | | |||||| || | || || | | ||||| || |||||||||||||| || ||||||||||| |||||| ||| |||||||| ||||| || |||||| | || ||||| || ||||| || || |
gtttgacgcgattgtcattttctattgtttgacaatctcttaggagtctgatggaattgccacatttgttcgcgccgagatgtttctggtacttgtgcttcatctctaaggaattgtaggttggactgaactataattatctgaaatcctctgttttgcggcgcagGTGAGCCATCACCCAATGATCGTGGCATGTCACTGCGAGGGTCGAGGATGGAAATTCTGGGGAGACAGCAACTTGAAAAGCAAGTTTTGGGGTCGTTCTA
upper sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
--caagacaatttggattttggtgtgaacaaaaaggatatgatttggcttttttattttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
| ||| || | | || | | | || || | || || | || | | | || | || ||||| | ||||| || |||||||||||||| ||||||||||| ||||| || || ||||| | ||| |||| ||| |||||||| |||||| | || ||||| || ||||| || || |
ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctcta-cgtgtttttatttttatttttatttttattttgta-cagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
caagacaatttggattttggtgtgaacaaaaaggatatgatttggctttttta-ttttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
|| ||| | |||| | || ||| | || || | || ||| | | || ||||||||||| || |||||| | || || |||||||||||||| || |||||| | ||||| || ||||| |||||||| ||||| |||||||| ||||
----------------------------------------gttagctagtcagcttttttctctgctacttga---tactgat-tttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttttattttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
tattaat putative branch site (score: 2)
tgtttttgcttcccct CT-rich tract
tattagaaattattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagacaatttggattttggtgtgaacaaaaaggatatgatttggcttttttattttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
caagaca
- - - - - - - - -tggtgtg
- - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - -tgatttg