Sequence
atgc intronic sequence ATGC exonic sequence...gtttttatcttttctgtaacagaaaatgaaccatactaaattgctgagttaggatttttgttttctttgagttctgtctctaattgtcgttttgcatcagAATCTTGGCTAATAGACAATCTGCACAAAGATCGCGAGTGAGGAAGCTGCAATACATATCAGAGCTTGAGAGAAGTGTAACTTCATTACAGGTTTGGGAT
Basic information
species | Glycine max |
transcript | GLYMA13G36870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G58120.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------gttttta-tcttttctg-taa--cagaaaatgaaccatactaaattgctgagttaggatt---tttgttttctttgagttctgtctctaattgtcgttttgcatcagAATCTTGGCTAATAGACAATCTGCACAAAGATCGCGAGTGAGGAAGCTGCAATACATATCAGAGCTTGAGAGAAGTGTAACTTCATTACAGGTTTGGGAT
|||| || | | |||| ||| | | | || |||| | | | |||| | | | | | | || ||| | | || |||| | |||||| || || ||||| ||||| ||||| ||||| | |||||||| |||||||||||||||||||||| || || || |||||||| |||
gtaattaacatttttatttactatttcccaaaaccccaaggaaggtcatgcatgcacgtacagtttataatagtatctgataattcgatacaccgtttttataaaatagttaaattagtgtcacatcgataaaatctaatttttgtttttg-ctgaaattttcta-cagAATTTTAGCAAATAGGCAATCAGCACAGAGATCAAGGGTGAGGAAATTGCAATACATATCAGAGCTTGAAAGGAGCGTTACTTCATTGCAG---------
upper sequence: GLYMA13G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S93_157V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttttatcttttctgtaacagaaaatgaaccatactaaattgctgagt-taggatttttgttt-----tctttgagttctgtctctaat-----tgtcgttttgcatcagAATCTTGGCTAATAGACAATCTGCACAAAGATCGCGAGTGAGGAAGCTGCAATACATATCAGAGCTTGAGAGAAGTGTAACTTCATTACAGGTTTGGGAT
||| | | | | | | | || ||||| | || | |||| || ||| || ||| |||| || | |||| |||||| | || || ||||| ||||| || ||||| || || | ||||||||||||||||||||||| || |||||||| | | | || |||
----------tttgtacagttcagagtttatgaggatagattgcagggtctcggatgttgacacaggaacggttgggtggtgtgattaatgtggatgagttgttgcg-cagAATTCTTGCCAACAGACAGTCTGCTCAGAGATCTCGTGTACGAAAGCTGCAATACATATCAGAGCTGGAAAGAAGTGTGAATGCGTTGCAG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttaggatttttgttttctttgagttctgtctctaattgtcgttttgcatcagAATCTTGGCTAATAGACAATCTGCACAAAGATCGCGAGTGAGGAAGCTGCAATACATATCAGAGCTTGAGAGAAGTGTAACTTCATTACAGGTTTGGGAT
ctctaat putative branch site (score: 3)
tcgtttt putative PPT
atttttgttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatcttttctgtaacagaaaatgaaccatactaaattgctgagttaggatttttgttttctttgagttctgtctctaattgtcgttttgcatcagAATCTTGGCTAATAGACAATCTGCACAAAGATCGCGAGTGAGGAAGCTGCAATACATATCAGAGCTTGAGAGAAGTGTAACTTCATTACAGGTTTGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - -ttctgta
- - - - - - - - - - - aaaatgaa
- - - - - - - - - - - - - - - ccatact
- - - - - - - - - - - - - - - - - - - - ttgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgtc