Sequence
atgc intronic sequence ATGC exonic sequence...actttaatttgcttttcttttttgtgaatcaagggatgtaactaaagttatcttttaaacttgttaattttcctacataaccagactcattttctctcagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
Basic information
species | Glycine max |
transcript | GLYMA05G30630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 5
--actttaa---tttgcttttcttttttgtgaatcaagggatgtaactaaagttatcttttaaacttgttaattttcctacataaccagactcattttctctcagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
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cagctttgaaccattgactttgttatttgtacgacaaaaaatagagtccctaagagatgaaaagaaaaataata-----atataactttattgttgcctttttagGAATTTAATAAGCATGACAGAGAGCCCAATAAGTACATAAAGCACTGGAGTGGCATCAAACCAAAAACTGGTGCCAAATACACCTGCGACATTGGATATG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------actttaatttgcttttcttttttgtgaatcaagggatgta-actaaagttatcttttaaacttgttaattttcctacataaccagactcattttctctcagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
| | || | || |||| | | | || |||| || || | | || | | | | | || | | |||| | | ||||| |||||||| ||||||||||| ||||| |||||||| || || |||| |||| | || |||||||| || |||||||| | || || | || ||||
gtaatccttagtggtgaatattcaagtcagataatattaatatatactcttctgaaaatttattactggcctgtatgctgaaatcgcttgaaaagaatataggaatattgata-aagaacattcatatggttgcagGAGTTTAATAAACATGACAAAGAACCAGCAAAGTATATTAAACAATGGAAAGGTGTAAAGCCAAAGACTGGTGCACCATACACTTGCGACGTGGGATATG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------actttaat-----ttgcttttcttttttgtgaatcaagggatgtaactaaagttatct-tttaaacttgttaattt---tcctacataacca-gactcattttctct-------cagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
|||| || | | | | | ||| | | | ||| || |||| | | | | | || | ||| | || || | | | |||||| ||| || ||||| || |||||||||||||||||||| | ||||| || ||||| ||||| || || ||||| ||||| || |||||||| || |||||| |||||||||
gtcatcttttctataagaacttctgacttaaagaaatataggatataaatggtgtaatttcattgatcattgtatagttttatgtccagaattttgaatctggatcttatttgatgatgactcagtttttcaatgattacagGAGTTCAATAAGCATGACAAAGAGCCTGGGAAGTACATAAAGCATTGGAGGGGCATCAAACCGAAGACAGGAGCACCATACTCTTGTGATGTTGGCTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttatcttttaaacttgttaattttcctacataaccagactcattttctctcagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
acataac putative branch site (score: 3)
ctcattttctctc putative PPT
tcttttaaacttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actttaatttgcttttcttttttgtgaatcaagggatgtaactaaagttatcttttaaacttgttaattttcctacataaccagactcattttctctcagGAATTTAATAAGCATGACAAAGAGCCAGCCAAGTATATCAAGCACTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCCTGTGATATTGGCTATG
- - - - -tgctttt
- - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctaca