Sequence
atgc intronic sequence ATGC exonic sequencegttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G35290.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
|||| ||| || | | | || |||| | | | || | || || || || | | | || | ||| |||| ||||||||||| | ||||||| ||||| ||||||||||||||||| ||||| |||| || |||||| || ||||| || | |||||||||||||
gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattc--tagatgatttcttattctgcttagatttaagGTGT---------------TAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA-------
upper sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
||| || | | ||| ||||| | || | | | || || | |||| | | | | || | || || ||| || ||||||||||||||| | ||||||| |||||||| |||||||||||||| || ||||||| || ||||||||||||||||| | |||||||||||||
-gtttggttacacatatttctgata-attgatgt--------ggctttg--tcgcacatattctag-atgattgcttatgctgcttagattt--aagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA-------
upper sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 11
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtattttt-gcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
|| | | | | ||||| ||| || | || || | ||||| |||| | ||| | | | |||| | | | | || |||||||||||||| | |||| ||||| | ||||| |||||||||| || ||||||| | |||||||||| ||||||||| | |||||||||||||
gtaaatagtgattctacgtttgaccaaattgttaatatatttcaggctgga-aaatttaactatgat----tttgtatctatgtttctctctcaaaagGTTTTAGCTGGAGACGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTA-------
upper sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 12
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
||||| | || || ||||| | | |||| | | | ||| ||| | | | ||| | | |||| || ||| |||||||||| || | ||||| ||||| || ||| ||||||| || ||||| |||| ||||||||| || ||||| ||| | ||||||||||| |
----gtattttatctattatttatatattataaattttgc---attgtcgattaatcaaa----------accgattatcac-------tttggaagGTTCTAGCTGGAGACATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCA------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
ggctaat putative branch site (score: 3)
taatgtgtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT