Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtatgtgtgtgtgtgtgtgtgtgtgtgtgtatacatatatgtatatatatgtatatcttattttccttatcctcacattcttcatttttctctacagGCAGTTGACATTAAACTCCTTGGGTCCCTTAACAGAGATGATTTAAAGAAAATCTGTGGGGATAATTTTCCTGAATGGATATCTTTTCCCATATATGAGC
Basic information
species | Glycine max |
transcript | GLYMA09G40290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtgtatgtgtgtgtgtgtgtgtgtgtgtgtgtatacatatatgtatatatatgtat--atcttattttccttatcctcacattcttcatttttctctacagGCAGTTGACATTAAACTCCTTGGGTCCCTTAACAGAGATGATTTAAAGAAAATCTGTGGGGATAATTTTCCTGAATGGATATCTTTTCCCATATATGAGC
||||| | || | || | | | || | | ||| | | | | |||| | | || || |||| |||||||||||| || ||||| || || || |||| |||||| ||||| |||||||| ||||| |||||||| ||| |||||||||| ||||| || ||| |
tgtgtgagaagtgacatg-gcttgctttactttctaagtttgagtagaggattttcttggccttacaataacagaatacgtatactcttaccttctg-acagGCAGTTGATATGAAACTACTAGGCTCTCTTAGCAGAGACGATTTGAAGAAAATTTGTGGTGATAATTTCCCTCAATGGATATCGTTTCCAGCATTTGAAC
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 2
tgtgtatgtgtgtgtgtgtgtgtgtgtgtgtgtatacatatatgtatatat-atgtatatcttattttccttatcctcacatt-cttcatttttctctacagGCAGTTGACATTAAACTCCTTGGGTCCCTTAACAGAGATGATTTAAAGAAAATCTGTGGGGATAATTTTCCTGAATGGATATCTTTTCCCATATATGAGC
| | | | | | | | | | ||| | | | || | | || ||| || | | ||| | |||||||||||| |||||||||||| || ||||||||||| |||||||||||||| ||||| |||||||| ||||| |||||||||||||||||||||||||| || | ||||| |
ttaatttatttaaat-tatactcctaaggaattatttttcacttcccagatgacttgtaccttgttctgatcccattcatttcatttcatttttctc-acagGCAGTTGATATAAAACTCCTTGGATCCCTTAACAGAGAAGATTTGAAGAAAATTTGTGGTGATAATTTTCCTGAATGGATATCTTTCCCTGTGTATGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatatgtatatcttattttccttatcctcacattcttcatttttctctacagGCAGTTGACATTAAACTCCTTGGGTCCCTTAACAGAGATGATTTAAAGAAAATCTGTGGGGATAATTTTCCTGAATGGATATCTTTTCCCATATATGAGC
tcctcac putative branch site (score: 2)
tcttattttccttatc CT-rich tract
tatgtatatcttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtatgtgtgtgtgtgtgtgtgtgtgtgtgtatacatatatgtatatatatgtatatcttattttccttatcctcacattcttcatttttctctacagGCAGTTGACATTAAACTCCTTGGGTCCCTTAACAGAGATGATTTAAAGAAAATCTGTGGGGATAATTTTCCTGAATGGATATCTTTTCCCATATATGAGC
- tgtatgt
- - - -gtgtgtg