Sequence
atgc intronic sequence ATGC exonic sequence...catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaatgttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
Basic information
species | Glycine max |
transcript | GLYMA11G36810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 7
catctacctcgggttgatttcac-tgggacaga-atggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaat---gttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
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-----acagaaaacacaatacatatgctatagttatcaatctctttccctttttttgggataacggattaatatggtgcctgatacagttgtttgatcagcacagGGTGTTCCTGATCGAGTGAACGATGAGGTTTTCATTGCAATGTCAAAGGCACTTAATTTCATAAATCCTGATGAGTTATCCATGCAGTGCATTCTGATTG
upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 7
-catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgt-tgcaaataatttgaaaataacaaaatgttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
|| | | || | ||||| | || | | | ||| | || | | | | | ||| ||| | | | | | |||| || ||||| || || | ||||||||| || || |||||||| |||||||| || ||||| ||||||||||| || || ||||| || || |||||||
agatatggttttactttccatttggaatacagatggtaatatatccttctattgtttatggagccatgtggtgcctgacacaat--tatttgatcagcacagGGTGTTCCTGATCGGGTGAACGATGAGGTTTTTATTGCAATGTCCAAGGCACTCAATTTCATAAATCCTGATGAGCTATCTATGCAGTGCATTTTGATTG
upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14210.1 (Arabidopsis thaliana), 3'ss of exon 7
catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaat-------gttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
|| || || || | || | | | ||||| || |||| | | | | || ||||| | | | || | | ||||| |||| ||||||||||| || ||||| |||||||| || || ||||| ||||| |||||||| || || ||||||||||| ||||||||||| || ||||| |
tgact-tttctagtccatgtggttgttgtggttt----cattgtcgtg-catgtgctttcactcagcagataataatacattctgattaattgtatacttgtc-cagGGAGTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAAACTTTATAAACCCTGATGAACTGTCAATGCAATGCATTTTGATAG
upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 7
-catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaatgttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG----
|||| | || | | | | || | | | | | | || | | |||||| | || | || | | ||||| |||| ||||||||||| || ||||| |||||||| || || ||||| ||||| |||||||| || || ||||||||||| ||||||||||| || ||||| |
ttttctagtccatgtggttgttgtggtttcattgtcgtgcatgtgctttcactcagcagataataat----acattctgattaattgtatacttgtc-cagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAAACTTTATAAACCCTGATGAACTGTCAATGCAATGCATTTTGATAGCTTT
upper sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 7
catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaatgttttctcct-----tgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
|| || | | | || || | | | | | | || | ||| | || || | || || ||||| || || ||||||| || | || |||| | ||||| |||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||| ||||||||||| ||||| |||||||||||||
gatttatgttgagctggattgaatt---ctgtgtcta-ttaagttaaggt-taaatttcagaaaaatttaaaatcaccaatggttttcttctctctctttttcagGGTATTCCTGATCGAGTAACAGATGAGGTTTTCATTGCCATGTCCAAGGCACTGAACTTCATAAATCCGGATGAACTTTCGATGCAGTGTATATTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtctgtgttgcaaataatttgaaaataacaaaatgttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
aaataac putative branch site (score: 2)
tgttttctccttgtt putative PPT
aaataatttgaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catctacctcgggttgatttcactgggacagaatggaaccttgtcatggtctgtgttgcaaataatttgaaaataacaaaatgttttctccttgttatagGGCGTACCTGAGCGAGTAACCGATGAGGTGTTCATAGCAATGTCGAAGGCACTAAACTTCATCAATCCTGATGAACTTTCAATGCAATGTATATTGATTG
- -ctacctc
- - - - - - - - - - - - - - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa