Sequence
atgc intronic sequence ATGC exonic sequence...ttaactgtggatttatttcaaaataaaatttcttttgaacttatcaatttttccttacctctcttgtaatatatgtttttctcatgcaattgtggcacagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC
Basic information
species | Glycine max |
transcript | GLYMA08G17960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
ttaactgtggatttatttcaaaataaaatttcttttgaacttatcaatttttccttacctctcttgtaatatatgtttttctcatgcaattgtggc-acagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC
| || | || | | | | || || | | || | || || || | | || | || || |||||| | ||||| || ||||| || || |||||| | |||||||| | ||| | ||||| |||||||||||||| |||||| |||||||||||||||| || || |||
tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtc-tgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
upper sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 3
ttaactgtggatttatttcaaaataaaatttcttttgaacttatca-atttttccttacctctcttgtaatatatgtt--tttctcatgcaattgtggcacagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC
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---ctcaaggaaatacttcattgtcattgtttgaaggtggtggtggtggttttatttttttccccttccatgtttcttcatatgtttttcatctatcatgcagGAGGTATATGAACAGCAGAAGGAATTAATTTTACTTGGAGAGAGGGTTGTACTTGCTACACTTGGTTTTGATCTTAATGTGCACCATCCATATAAACCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttttccttacctctcttgtaatatatgtttttctcatgcaattgtggcacagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC
tccttac putative branch site (score: 2)
ttgtaatatatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaactgtggatttatttcaaaataaaatttcttttgaacttatcaatttttccttacctctcttgtaatatatgtttttctcatgcaattgtggcacagGATGTGTATGAACAGCATAAAGAATTAATTTTACTGGGAGAGAGGGTTGTTCTTGCAACTCTTGGTTTTGATCTGAATGTGCATCATCCTTATAAACCTC
- -actgtgg
- - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca