Sequence
atgc intronic sequence ATGC exonic sequence...tgaatctgttctgccatgtaattattttatgttgaatgcttattattttgaattttcccacatgtttccattggttcattgattaaatatttacttgcagCATTATATGCCTCCCTATGGCACTCCACCACATCCCTATGTTGCAATGTATCCCCATGGTGGCATATATGCTCATCCATCTATTCCTCCG
Basic information
species | Glycine max |
transcript | GLYMA08G34280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------tgaatctgttctgccatgtaattattttatgttgaatgcttattattttgaattttcccacatgtttccattggttcattgattaaatattta--cttgcagCATTATATGCCTCCCTATGGCACTCCACCACATCCCTATGTTGCAATGTATCCCCATGGTGGCATATATGCTCATCCATCTATTCCTCCG
|| | | | | | | ||| |||| |||| | || || ||| || || || |||| || | || | | ||| | ||||||||| |||||||| ||||| ||||| || ||||| ||||||||||||||||||| |||||||| || || ||||| || || ||||||
gtgaactggcttacgctttatcgctttttactgtgatgtctatcggtgttcagagtgctggaaaattgcaacattcttattgacttataacgaat--tcgttcagctgtctttcatcatat-ctttgattgattactgaatgagacattaaattttgcagCATATGATGCCTCCTTATGGAACTCCGCCTCATCCTTATGTTGCAATGTATCCCCCAGGTGGCATGTACGCACATCCTTCAATGCCTCCG
upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 3'ss of exon 4
------tgaatctgttctgccatgtaattattttatgttgaatgcttattattttgaattttcccacatgtttccattggttcattgattaaatatttacttgcagCATTATATGCCTCCCTATGGCACTCCACCACATCCCTATGTTGCAATGTATCCCCATGGTGGCATATATGCTCATCCATCTATTCCTCCG
| ||| ||| | || | | |||||| | | | ||| || || | | | |||| | | || | | | | ||| |||||||||| |||||||| ||||| || ||||||||||| ||||||||||||||||||| ||||||| ||||||||||||||||||||||||||
agtgcttcaatttgtcttttca-gcacctatttttttct---tctttaacccaatgttttgtttgata-gtttgtacagttttaaaaaattt-tgtttgcttgcagCATCTAATGCCTCCATATGGTACCCCACCACATCCATATGTTGCAATGTATCCCCCTGGTGGCTTATATGCTCATCCATCTATTCCTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaattttcccacatgtttccattggttcattgattaaatatttacttgcagCATTATATGCCTCCCTATGGCACTCCACCACATCCCTATGTTGCAATGTATCCCCATGGTGGCATATATGCTCATCCATCTATTCCTCCG
cattgat putative branch site (score: 4)
tttactt putative PPT
ttcattgattaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatctgttctgccatgtaattattttatgttgaatgcttattattttgaattttcccacatgtttccattggttcattgattaaatatttacttgcagCATTATATGCCTCCCTATGGCACTCCACCACATCCCTATGTTGCAATGTATCCCCATGGTGGCATATATGCTCATCCATCTATTCCTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - ctgccat
- - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttcc