Sequence
atgc intronic sequence ATGC exonic sequencegttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
Basic information
species | Glycine max |
transcript | GLYMA01G14800.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 12
gttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
||| ||| || | | | | | || ||| | | |||| | || | || | |||| || || ||||||| |||||||| ||||| || |||||||| |||||||||||||||||||| ||||||||||| |||
gtttgttttg--ttatctgttgtatttttctaaatctatcatt----tgtgaactttaaagtgtaaattttgatcgcagACAATTATTTCTGGGATGGGTGAGCTGCATTTGGATATCTATGTTGAACGCATCAGGAGAGAGTACAAG
upper sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------gttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
|| || | | | | | |||| | |||| | |||| | | | ||| | || || || |||| || |||||||| ||||||||| ||||||| || ||||||||||||||||| | ||||| ||||||
gtatcatctaaaaactcttttgcttctcagcacctctctcttaattcaccccatagtatt-taacattgatgattcttccatttatccttcatg-ggacagACGATTATTTCTGGTATGGGGGAATTGCATTTGGACATCTATGTTGAACGCATGCGAAGAGAATATAAG
upper sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------gttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatc-ttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
| | | | | | || || | | || | |||||| | || | | || || ||||| || |||| || |||||||| ||||||||| ||||||| || ||||||||||||||||| ||||||| ||||||
gtatcatctaaaaactcttttgcttctcagcaccactctcttaattcaccccattagtatttaacattgaggattcttccatttatccgtaatg-----ggacagACGATTATTTCTGGTATGGGGGAATTGCATTTGGACATCTATGTTGAACGCATGCGGAGAGAATATAAG
upper sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 12
gttatcttta----atttttttatcattctcttttaagtaaaacatt--attgtttgtatcttgattagtaa----tttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
||| |||| || ||| || || || || || | || || | || | | || || || ||||||| |||||||||||||| || |||||||| || || || |||||||||||| |||| |||||||||
gtttaatttatgacatgcatttcacacattccttagaggaagaagttttatcatgcctaaccatgacatcaaaatgctttcttgtgcagACAATTATTTCTGGAATGGGAGAGCTGCATTTGGACATTTACGTTGAACGCATTCGGAGGGAGTATAAG
upper sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S100_33V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------gttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatctt--gattagtaattt--ctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
|| |||||||||| | || | | |||| | | | || | | | | || | || |||| || ||||| |||||||| || |||||| ||||||||||||| ||||||||| | | || || |||
actgtgcagttggttgattttactttaattttgtagaagttgtgatagaagttcagcggatcgatctgaagcgcagggacgggggttgggttttgtgcagACCATTATTTCGGGAATGGGAGAGCTGCATCTAGATATCTATGTGGAACGCATTCGTCGTGAATACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
tcttgat putative branch site (score: 4)
tttctgt putative PPT
ttaagtaaaacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA