Sequence
atgc intronic sequence ATGC exonic sequence...tttgtttagttgtattttgaaaactaaaagcagcttttaaaataaaaatcaaacgcgtccttagtcttttagtattaataaactactttttcacacgcagTTTACCAGGCTGGGCCATACTAAACTGCGGGAGAATGCCATCATGATCACTAGTACCATCACTGTTGTACTCTTCAGCACATTG
Basic information
species | Glycine max |
transcript | GLYMA17G02560.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 11
tttgtttagttgtattttgaaaactaaaagcagcttttaaaataaaaatcaaacgcgtccttagtcttttagtattaa-taaactactttttcacacgcagTTTACCAGGCTGGGCCATACTAAACTGCGGGAGAATGCCATCATGATCACTAGTACCATCACTGTTGTACTCTTCAGCACATTG
| || ||| | || | ||||| || | ||| || | ||| | | || |||| ||| |||||| || ||| ||||| ||| |||| | ||||| ||||||||||||||||| ||||||||||| || |||||||| ||
-taacttgtttgaggctggattttttttgtttgctttcgtgtattaactattgttcgtaattcatgctttgatctgaaacttgtcacttcgacacttgcagTTCACAAGGTCAGGCCACACTCAACTCCCTAGTAATGCTATCATGATCACTAGTACAATCACTGTTGTTCTTTTCAGCACGATG
upper sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 12
tttgtttagttgtattttgaaaactaaaagcagcttttaaaataaaaatcaaacgcgtccttagtcttttagtattaataaactactttt-----tcaca-cgcagTTTACCAGGCTGGGCCATACTAAACTGCGGGAGAATGCCATCATGATCACTAGTACCATCACTGTTGTACTCTTCAGCACATTG
||| | | | ||||| ||| | | | || ||| | ||| | || || | | || ||| | | ||| | |||| || | || || || || | | | ||| || ||||||||||| ||||||||||||||||| || ||||| || ||
--------gttttgatccgtgaactacaagaaacaaagataaaaaagtgatctttgggttttaataagttcccatgacttaatctcttctctctgttacatcatagTTCACAACTTCAGGACACACCAAGGTTCTTGGGAACGCTATCATGATCACCAGTACCATCACTGTTGTTCTTTTCAGTACTGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcaaacgcgtccttagtcttttagtattaataaactactttttcacacgcagTTTACCAGGCTGGGCCATACTAAACTGCGGGAGAATGCCATCATGATCACTAGTACCATCACTGTTGTACTCTTCAGCACATTG
tattaat putative branch site (score: 2)
ctactttttc putative PPT
tcttttagtattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtttagttgtattttgaaaactaaaagcagcttttaaaataaaaatcaaacgcgtccttagtcttttagtattaataaactactttttcacacgcagTTTACCAGGCTGGGCCATACTAAACTGCGGGAGAATGCCATCATGATCACTAGTACCATCACTGTTGTACTCTTCAGCACATTG
- - - - - - - - - - - - - - -gcagctt
- - - - - - - - - - - - - - - - - - - aaaataa