Sequence
atgc intronic sequence ATGC exonic sequencegttagttagggaatctttcttagattgcttgctgtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
Basic information
species | Glycine max |
transcript | GLYMA13G28120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
gttagttagggaatctttcttagattgcttgctgtagcatatatatat-atttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
| || || | | | | || | ||| | | | || || || | |||| || | | |||| ||| | || || | ||| | ||||||||| |||||||| ||||| || |||||||| ||||| ||||||||||| || || || || || || || ||||| ||||| ||||| |||||||
----------------------agtagcctgatatgactgctccatctcattattcaatatattttgtta-tactagaattttactgatatgacagctgtctttca--ttatttgtttact-gcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagttagggaatctttcttagattgcttgctgtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
|| |||| | ||| | || | |||| || | ||| | ||||| | || | |||| || || ||| ||| ||||| ||||| || ||||| || || |||||||| || ||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || |||||
---------------------------gttaagctagcgagca-ataaaatt-tcattgattagtataagtt-tatgattatct---ttctgaaaatactttt----tttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gttagttagggaatctttcttagatt-------gcttgct---gtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttg----aacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
|| ||| | | |||| ||| | | ||||| | |||| || ||| | |||| | | || || | || | | | ||||||||| | | ||||| ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || |||||||||||||| ||||| || || ||
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagta-ataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
tcttaat putative branch site (score: 3)
aaattatatgatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttagggaatctttcttagattgcttgctgtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttgaacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA