Sequence
atgc intronic sequence ATGC exonic sequence...ttgacattttagttcttaccgtgctatattaaaattgtgtttgcctctgcattttttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
Basic information
species | Glycine max |
transcript | GLYMA05G33560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 6
-ttgacatttt---agttcttaccgtgctatattaaaattgtgtttgcctctgcattttttac-ttgaatgat---------tgtcagtaaatt-tattgtttattaa---------tctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
|| ||| || |||| | || | ||||||| | ||| ||||||| || | |||| ||| | | | | | | ||||||| |||| | || || ||| || ||||||||| ||||| ||||| ||| | ||||||||||||||||||| |||| |||||||| ||||| | |
gttagtgtttccagagaccttaaaggaacattccctgaactccaaaaactctgcaactcttaagttgaatggaagaaacatatgctaataaagaacattctctctggaaaaattgtttgttcagGAAAGCAACAGATTGGAGTACCTGATACCAAAAAGAACATCGTTGAGACATCGGCTGCCAATGGGAGACCAAGGATTCACAGACTTTGTGGCTCATCTTC
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
ttgacattttagttcttaccg-tgctatattaaaattgtgtttgcctctgcattttttact-tgaatgattgtcag--taaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
| ||| |||| || | |||| | | | || | | |||| ||| | | | | || | | | |||| | | ||| ||||| |||||| | | |||||| | | ||||||||||||||||||||||| | ||||||||||| |||||||||||||| ||||||||| |||| |||
---atctttgtgttcatattactcctatttctgcaacttcctt-tttatttatttattattattattaatcctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcattttttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
tattaat putative branch site (score: 2)
attgtcagtaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgacattttagttcttaccgtgctatattaaaattgtgtttgcctctgcattttttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGGTACCAAAAAAGACATCCTTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
- - - - - - - - -accgtgc
- - - - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga