Sequence
atgc intronic sequence ATGC exonic sequence...aaataaaaggcctgagaacagtgtaggaaaagtcattctcatgcatgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgttgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
Basic information
species | Glycine max |
transcript | GLYMA05G02460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G02460.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50150.1 (Arabidopsis thaliana), 3'ss of exon 3
aaataaaaggc-ctgagaacagtgtaggaa---aagtcattctcatgcatgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgt-tgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
| || | ||| | | || ||| | || ||| | ||| | | | |||||| || || | | || | | | |||||||||| || || | |||||||||||| ||||||| |||||| ||||||||||| ||||||||| |||| | || |||||| | || || || ||||| |
atattcttgatattgaagataaagtgtgaacttaggttatttttatg-----gtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
upper sequence: GLYMA05G02460.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g08870.t01 (Vitis vinifera), 3'ss of exon 3
----aaataaaaggcctgagaacagtgtaggaaaagtcattctcatgcatgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgttgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
|||| || ||| | || | ||| ||| | | | | | | || | | | || ||| | | | |||||||||||||||||| ||| ||||||||||| || | |||||| || || ||||| || |||||| |||| ||| | |||| ||| |||||||| ||||
taagaaatgaagaaactgtgttca---tgtcaaatttcactgaaactgcagtcgacattcagaattgtgggtgcccctt-ttactgataatcttttgcctgcagCATGCAGTTGTTTTTGTCAATGGAGATCAGTATTATGGAGCCAAGGCCAGCATTAATGTGTGGGCGCCCCACGTGGCCGATCAATATGAATTCAGCTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgttgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
ttttgac putative branch site (score: 3)
tgtatgtttaatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaataaaaggcctgagaacagtgtaggaaaagtcattctcatgcatgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgttgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
aaataaa
- - - - ggcctga
- - - - - - - - - - gtgtagg
- - - - - - - - - - - - - - - - -cattctc
- - - - - - - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaca