Sequence
atgc intronic sequence ATGC exonic sequence...tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
Basic information
species | Glycine max |
transcript | GLYMA12G03260.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 4
---------tttgcacatcatgtgtacacttttgttgtttatgc-aggatttttaaaataaaaattta-atgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
||| || || || | | || || | | | | | || |||||| | |||| || | | | ||||||| |||||||| || || |||||||||||||||| ||||| |||||||| ||||| | |||||| || || ||||| |||||||| ||
attgactaaattgatcaacagtaataaaagcatcatggttgtaccatgtactatattataaaaccgcatatgtgatgataaataatttaatgttttcc-----------agGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACTAAGCCAGGTCACAATGAAGGTGGTGTGAG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
--------tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
| |||| | || ||| | ||| | || | | | || | | || |||| ||| | |||| | | |||| |||||||| || || |||||||||||||||| ||||| |||||||| ||||| | ||||| || || ||||| |||||||| ||
taaattgatctgca-gtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatact-tcatttaatgttttcc------agGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
---tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatt-taatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
| |||| | | || | | || | | | | ||| | || | ||| || ||| ||||| || | ||| | || | |||||||| ||| |||| ||||| || || ||||| |||||||||||||| ||||| ||||| || ||||| |||||||| ||
tatgctatgtgtcat-cgagtagcttaactaag-aggctgcactgtgtgaatgtgagttcttatgcat-aatgcactttttctt-tttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
----tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
|| ||| |||| | | | | || | | || |||| | || ||| || ||| || ||| || | || || | |||||||| || || || |||||||||||||| || |||||||| |||||||| ||||||||||| |||||||| |||||||| ||
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgctt--cttccttatgattatgagttgtt--tcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
upper sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S148_65V6.2 (Physcomitrella patens), 3'ss of exon 3
tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaata---aaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
| ||| || | || | |||| | || |||||||| | || | | ||||| | || | ||| | | |||||| | || |||||||| || || |||||||||||||| || ||||| || ||||||||||| || ||||| ||||| || |||| ||
--ttcacgtcttcaaaggcattctcttgtgt-tgaaggattttctagatccgcatagtttaagggatccgccaagttttccttattttttatggttcatgcagGTGTGGCAACATAAATTGGGCAAAGCGCACAAAATGTAACATCTGCAACACTGCCAAACCTGGTTTCAATGAAGGCGGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
aattgac putative branch site (score: 3)
ctttctcatgtttttt CT-rich tract
tttctcatgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
- - cacatca
- - - - - -tgtgtac
- - - - - - - - - - - - - - tttatgc
- - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga