Sequence
atgc intronic sequence ATGC exonic sequencegtgagatattattaatttgatatgatccattaattaattgcattcctcatgtagctcttaatgaatgaattgcatgcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
Basic information
species | Glycine max |
transcript | GLYMA02G48080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 3
-----------gtgagatattattaatttgatatgat--ccattaattaattgcattcctcatgtagctcttaatgaatgaattgcatg----catgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
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tccagattgtgatagaatcttttatgacagacagcatgcttatatatcgtttgatctggttgcaaacttgcaaatatacttacttttttatctctcccagTGTGTCCCACGACCCTCAAAAGAATATGCAGGCAACATGGTATAACCCGCTGGCCATCACGAAAGATCAAGAAGGTAGACCACTCTCTAAGAAAGCTCCA
upper sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35270.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtgagatattattaatttgatatgatccattaattaattgcattcctcatg-tagctc-ttaatgaa---tgaattgcatgcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
| ||| | | | || |||| | || ||| | || | || || | | | | | || |||| |||||| ||||| || || ||||||| |||||||||||||| || ||||| ||||||||||| |||| || ||||| |||||||| || || |||||||| ||
gtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgt-tgcagTTTGTCCAACTACCTTGAAAAGAATATGCAGACAACACGGGATAACACGATGGCCTTCCCGGAAGATCAAGAAAGTGGGGCATTCATTAAAGAAACTCCA
upper sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17150.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------gtgagatattattaat-ttgatatgatccattaattaattgcattcctcatgtagctcttaatgaatgaattgcatgcat-gcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
| | || || || || || || ||| || | | | | ||| | | | | || | ||||| ||||| || || |||||||||||||||| |||||||| |||| ||||||||| || | ||||| |||||||| ||||| || ||||||||||| ||
tggtagtggatcaatcatcatgctctacaaacattttcatcatg-gctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
upper sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtgagatattattaatttgatatgatccattaattaattgcattc--ctcatgtagctcttaatgaa-tgaattgcat-gcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
| | || || | || |||| || ||| || | | |||| || | || | | || ||| | | ||||||||| ||||| || ||||||||||||||||| |||||||| || || || |||||||| |||| || ||||| || || ||||| || | |||||| ||
gcatctatccattaagattatcagttcttgctatgtggtgatgca--aataggctgtttccagctcac-taccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaattaattgcattcctcatgtagctcttaatgaatgaattgcatgcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
tcttaat putative branch site (score: 3)
ttaatgaatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatattattaatttgatatgatccattaattaattgcattcctcatgtagctcttaatgaatgaattgcatgcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA