Sequence
atgc intronic sequence ATGC exonic sequence...aattggcatgatacatctcaagcttgcagcctgataaaatataagccatatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
Basic information
species | Glycine max |
transcript | GLYMA03G34340.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 6
aattggcatgatacatctcaagcttgcagcctgataaaatataagccatatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
| ||| | | ||| || | ||| | | || | | | || | | | || | || | | | |||||||||||||| ||| || | |||||| | |||||| || |||||||||||||| || || ||||| || ||||||||||| ||||| | || |
-gtgagcacgttttctctaaaaatcatgtttct------tatgtgttctgttatgtggtcacattacactcatctcagatactgttc-actgttcttcagGCAGATTGAAACAGATAGTGATTTTTTGAGAACACAGCGGATAATGGATTACAGCCTACTGCTTGGTGTCCATTATAGAGCTCCACAGCACTTGCGGACA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 6
aattggcatgatacatctcaagcttgcagcctgataaaatat-aagccatatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
| |||| | ||| | | | | | | | | || | | | || ||| |||| | || || | ||| |||||||||| |||||| | |||||| | |||||| || |||||||||||||| || || ||||| || ||||||||||| ||||| | || |
-gtgagcatattttctctagaaatgatgtttatgtgttctgttatgtgacgacattacacttatctcaaaatactg--ttgattattc--------ttcagACAGATTGAAACAGACAGTGATTTTTTGAGAACACAGCGGATAATGGATTACAGCCTACTGCTTGGTGTCCATTATAGAGCTCCACAGCACTTGCGGACA
upper sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 5
----aattggcatg---atacatctcaagcttgcagcctgataaaatataagcca-tatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
| || | || | || ||| | || || || | | | || | | | | || | | | || | || |||||||||||||||| || ||||| |||||||||||||||||||||||||||||||| |||||| | || ||||| || ||| |||| ||||| ||||| || |||
gcatagtttggctgcaagtgaatgtcaggtatgtagtctcttttcttgcatatcaatgctcctgtcattggttatagtttccttgta--tatctt------tatgcagGCAGATTGAGATTGACAGTAAATTTTTGGAAGCACAGCACATTATGGATTATAGCCTTTTACTGGGTGTGCATTATCGAGCCCCCCAACATCTGCGGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
ttctaat putative branch site (score: 2)
tttttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattggcatgatacatctcaagcttgcagcctgataaaatataagccatatttttctaatgaactgcaaaaactgaatagacagctccaaaaatatgcagGCAGATTGAAATAGACAGCAAATTTTTGGAAGCACAGCACATTATGGATTACAGCCTTCTTCTAGGTGTTCACTATAGAGCTCCCCAGCATCTACGTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - -gcatgat
- - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - -cctgata
- - - - - - - - - - - - - - - - - - aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccaa