Sequence
atgc intronic sequence ATGC exonic sequence...gatttgatttttgttttgaaagatactaggggtggatatagaatcacgtggtgtcaattaactacaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA
Basic information
species | Glycine max |
transcript | GLYMA09G36820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 2
lower sequence: 13113.m00212 (Oryza sativa), 3'ss of exon 2
gatttgatttttgttttgaaagatactaggggtggata---tagaatcacgtggtgtcaattaa-ctacaaatgcttatg-atttatatatgaatgtatt--tgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA
|| | ||| || || | | | | ||| | | || | | | || | | | | || || | | | |||| || || |||||||||||||| ||||||||||||||| || |||||||| | | || || | | |||
-------ttgatagtttagaatattttcccttctcctcctctcgcatcgatcgattgcattagggtttcgaactttcacctactgatcgatcgccgactcgccgcagGAGGACGGATGGGTGGTGTGCAGGGTGTTCAAGAAGAAGTGCTTCTTCAAGATCGGCGGCGGCGGCGGCGGCGAGGGGAGCGGGGGGAGCCAGGGAGGGG
upper sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gatttgatttttgttttgaaagatactaggggtggatatagaatcacgtggtgtcaattaactacaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA
| | || || | | | || | | | | | ||||| | ||||| | | | | | || | ||| | | | | ||||||||||||| |||||||| || |||||||| | |||||| ||||| |||||| | | |||||||||| | || | ||| || ||||| ||||
actgcactgtatattatgctgcaataaattcaatttattggt-tagaa--atgtggt-ctattatatttaatccatttgcaacatattt-tatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
upper sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
gatttgatttttgttttgaaagatact-aggggtggatatagaatca--cgtggtgtcaattaac------tacaaatg---cttatgatttata-tatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAA-ACCAG-ATCACCAAATCAACA
| |||| || || || | ||| || ||| || | || || ||| || | |||||| || | ||| || || |||||| || |||| ||||| |||||||||||||| || |||||||||||||| |||||||| ||| || ||||| || | | |||| || || | |
--------gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgtggtgtcaattaactacaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA
aattaac putative branch site (score: 2)
ttatgatttatatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatttgatttttgttttgaaagatactaggggtggatatagaatcacgtggtgtcaattaactacaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAAACCAGATCACCAAATCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - -tgttttg
- - - - - - - - - - - - - - -gggtgga
- - - - - - - - - - - - - - - - - - - - - - - -gtggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg