Sequence
atgc intronic sequence ATGC exonic sequence...gcaaagaaatctttaggcttcatgtataatctaaatgcaattgggaatgttttgcacattctgttttaaaatttaacctttatttttcactttctttcagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
Basic information
species | Glycine max |
transcript | GLYMA13G44940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g56320.1 (Oryza sativa), 3'ss of exon 4
---gcaaagaaatctttagg-cttcatgtataatctaaat--gcaattgggaatgttt-----tgcacattctgttttaaaatttaacctttatttttcactttcttt--------cagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
| | ||||| || ||| |||| || | ||| ||| || | | ||| | |||| | | ||||||| | | || |||| || ||||| |||||||| ||||||||| |||| || || |||||||||||| || ||||| |||||||||| |||||||||||||| ||||||||
gtagtgcacttctctttgtttctctctgtgtaattgggatatgaaataatacatggttgtagttcaatattattctttagttcgttttcaatatttttgaggaacattgcacaatgcagGAATCTGGGGTGGAAAAGGCCAAGGGAAAACATTCCAGACTGAACTTATATTTAGAGCAATGGGTGTTGAACCTGTTATTATGTCTGCTGGAGAACTAGA
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73110.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaaagaaatctttaggcttcatgtataatctaaatgcaattgggaatgttttgcacattctgttttaaaatttaacctttatttttcactttctttcagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
| || ||| | || |||| | | | | || ||| | | ||||||| | | | || || | | | | ||||| | | |||||| |||||||| ||||| ||||| ||| ||||||| || ||||||||||| | | |||||| ||||||| || || |||||||| || || | ||
gtaatgaatgcctt---cttcttctctg-tttagtagcagtgtttgaaattttgca-accatctcttgaacatggatgtgt-ttttttatggctgcttagGTATATGGGGAGGTAAAGGACAAGGCAAAACATTTCAGACTGAACTTATATTCAAAACAATGGGAGTTGAACCAGTTATAATGTCTGCAGGAGAGTTGGA
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01270.t01 (Vitis vinifera), 3'ss of exon 4
-gcaaagaaatctttaggcttcatgtataatctaaatgcaattgggaatgttttgcacattctgttttaaaatttaacctttatttttcactttcttt-cagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
|| | ||| ||||||| ||| ||| | || | | | | || | | | | | ||| || ||| |||| ||||||||||||||||| || || ||||||||||||||||||||||| || ||||| |||||||| |||||||| |||||||||||||||||||| ||
catgaatggaaaattaa-tttcatgtgcttatggttatttatttagaacatatttcctgataactaatgaagct-agtttaattatatcatttattttgcagGCATTTGGGGAGGAAAAGGTCAGGGAAAATCATTTCAAACAGAACTTATTTTCCAGGCCATGGGAATAGAACCTGTCATTATGTCTGCTGGGGAACTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttttgcacattctgttttaaaatttaacctttatttttcactttctttcagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
atttaac putative branch site (score: 3)
tttaacctttattttt CT-rich tract
ttttaaaatttaacct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaagaaatctttaggcttcatgtataatctaaatgcaattgggaatgttttgcacattctgttttaaaatttaacctttatttttcactttctttcagGTATTTGGGGAGGAAAAGGGCAAGGGAAATCATTTCAAACAGAACTTATATTTCAGGCTATGGGAATTGAACCTGTAATTATGTCTGCTGGGGAACTAGA
- aaagaaa
- - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - -ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcacat