Sequence
atgc intronic sequence ATGC exonic sequencegtcacatgttccacaaatgatgcctactgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
Basic information
species | Glycine max |
transcript | GLYMA08G43450.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43450.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g48830.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------gtcacatgttccacaaatgatgccta---ctgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
| || || | | | | |||| || || || || |||| | || ||||||||| | |||||| ||| | || |||||||||||| |||||||||||||||| | || ||| | || |||||
gtgagtcacacaatatactaattggtcttttattggaccaccttcagcatcccttcatatatattttttacttctcgtttgattttgatcttcattacccaatatttc--agGCACAGACTGAGGTTGAAAGGTTGGATCAGCTAAAATACAGCAAGATGAAAGAAATAGCTTTTAAGAAGCAAGCCATACTGGAAGATATTTATGCTAGCA
upper sequence: GLYMA08G43450.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------gtcacatgttcca---caaatgatgcctactgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
||| | || | || | ||| | || || || | ||| || || |||||||||| ||||||||||| |||||| | |||| |||||| | | | |||||||||||||| || ||||||||| ||||||||| |||||||||| | ||
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatatt-catgtaaaat-ttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
upper sequence: GLYMA08G43450.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------gtcaca-tgttccacaaatgatgcc-------tactgatttttctt-gtttta----tgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
| | |||| | || |||| || | ||||| ||| ||||| |||| |||||||| |||||||||||||||||| |||| | |||||| | ||||||||| ||||||||||| |||| ||||| ||||| ||| |||||| ||||| ||
gtatttggcttcagaacagtaatgcttaattttggcttcagaatagtaatgtttaatggataatgctggcagtttattcattttactttgttttccttttgttgctaagGCTGAGGTGGAAGTTGAAAGGCTTGATCAACTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAGGCAAGCTGAGCTCGAAGAGATATTTGCCCGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcacatgttccacaaatgatgcctactgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
tactgat putative branch site (score: 2)
tttttcttgttttat CT-rich tract
atttttcttgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcacatgttccacaaatgatgcctactgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT