Sequence
atgc intronic sequence ATGC exonic sequence...tccatatgattgtcgttctgggagaagtctttataagtttgttcattatgtgttctatctgtccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA13G17510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 2
-tccatatgattgtcgttctgggagaagtctttataagtttgttcattatgtgttctatctg-tccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
| || || | | || || | || | || || | | | || | || ||| |||| | ||| || ||| ||| ||||||||||| | || || ||||||||||| ||||| |||||||| ||||||||||| ||| | || | || || ||||| | || || ||||| ||||| |
ttttatcaagttattggcctttgaaatttcacactttattactttttcgtatcttattagtgctccatgtaagagcttcat--tttggttctttatttccagTTTTGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCATCGGCGCATGGCGTCACGGAAAGAAAAGCCACGCATCCTGATCCTTGGTGGTGCACTT
upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
-tccatatgattgtcgt---tctgggagaagtctttataagtttgttcattatgtgttctatctgtccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
| ||| | |||| || | | || |||||| | ||| ||| || | | | || | || | || || ||| || ||||| || ||||||||||| ||||| || ||||||||||||||||||||||| |||| || || || || ||| | ||||| |||||||| ||| ||
cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattac-tgattgaactgggatggtatt---tttttagTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
upper sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 2
tccatatgattgtcgttctgggagaagtctttataagtttgttcattatgtgttctatctgtccctgtatggtcttgatgttttagttttttat-ttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
|| ||| || || | | | | || | | | | | ||| | || | | | ||| ||||| ||| ||| |||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||||||| | ||||| |||||||||||| ||| | || ||||| ||| ||
-acaattgacaatcaccttgcaaacactttaactagaggatgctgtcaatttctttttctttttctttgtactgatgaaattttaatttcatatcttccagTATGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGACGAATGACATCTAAAATAAGTAAACCACGTTTCCTACTCCTCGGAGGAGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtgttctatctgtccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
tcttgat putative branch site (score: 4)
ttttttatttcc putative PPT
ttgatgttttagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccatatgattgtcgttctgggagaagtctttataagtttgttcattatgtgttctatctgtccctgtatggtcttgatgttttagttttttatttccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGAGGTGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
-ccatatg
- - - - - - - gttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg