Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctgctttgcttttataagccaaactgttgagttttaattgttcttgaccatatatattgtttgcttaatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
Basic information
species | Glycine max |
transcript | GLYMA09G36050.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G63460.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttctgctttgcttttataagccaaactgttgagttttaattgttcttgaccatatatattgtttgcttaatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
| | | || | | | | ||||| |||| | || | | ||| | || | ||| | | | || || || | | |||||||||||||||||||||||| || ||||||| ||||| ||||||||||| ||||||||||||||||| ||||| || | || |||||||| |
-----gtgagttgtgtctctctgcattattttgttg---cttaacgctgttt---tgtttttatcactc-ctcattttca---tgtgtgcgtgcttctttttttcttagGTTCGTGGTCTTGAGTTTAATGCTATCAGCTCAAATCTACTTGCTTCTGGGGCTGATGATGGTGAAATTTGCATTTGGGACTTATTAAAGCCTTCAGAGC
upper sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G18830.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttctgctttgcttttataagccaaactgttgagttttaattgttcttgaccatatatattgtttgcttaatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
| || | || ||||| || || || | |||||||| | | | |||| | | || | | ||| | | |||||||||||||||| |||||||| | | ||||||| ||||| ||||||||||| |||||| | |||| || |||||||| | ||||||||| | |
--------------------gtgagtttgtatcttctgttttg-ttttttttcccgatatatatacatcgtt--atttgatgtg-tacatgcattgttttgtaatatagGTTCGTGGTCTTGAATTTAATGTTAAGTCTCCAAATCAACTTGCTTCTGGGGCTGATGATGGTACAGTTTGTATTTGGGATTTAGCAAATCCTTCAAAGC
upper sequence: GLYMA09G36050.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 2
gtaagttctgctttgcttttataagccaaactgttgagttttaat------tgttcttgaccatatatattgtttgctt-aatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
||||||| | || | ||| | | || || | || || || ||| ||| || || || ||||| | | | | || || ||||||||||||||||||| ||||||| ||||||||||| || ||||| ||||| ||||| || || || |||||||| |||||||||| ||| ||||||
gtaagttttcctccacatttttcatccgttttgggtcttcttgatgtcgggcatttgggacggtattgggtgcttatttgaattttttttttttccctttaaattctaaaattcagGTTCGTGGTCTTGAATTTAATGCAATTGCACCAAACCTACTTGCTTCTGGAGCTGATGAAGGCGAGATTTGCATTTGGGATTTGGCAGCACCTGCAGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatatatattgtttgcttaatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
gcttaat putative branch site (score: 4)
tcttatatttttctt putative PPT
ttaatttaaaatccta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctgctttgcttttataagccaaactgttgagttttaattgttcttgaccatatatattgtttgcttaatttaaaatcctatcttatatttttcttgtttcagGTTCGTGGTCTTGAGTTTAATGTCATTGCACCAAATCTTCTTGCATCTGGGGCTGAGGATGGTGAAATTTGCATATGGGATTTGGTCAATCCTTCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG