Sequence
atgc intronic sequence ATGC exonic sequence...ataatctgagagttttagaggaatttattaaattgttggatgaccaccaattttgattatctgtaaagatgattttaatctcttctgattgttatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT
Basic information
species | Glycine max |
transcript | GLYMA01G40860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 3
-----------------------------ataatctgagagttttagaggaattt--attaaattgttggatgaccaccaattttgattatc-tgtaaagatgattttaatctcttctgattgt-tatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT
| | ||| || || | || ||| ||| | | || || || ||| | | | || | ||| ||||| | | ||||||||||||||| || ||||| ||||| || ||| || |||||| |||||||| |||||||||| ||||||||||| ||||| || |||||||
gtgaggactgatctatcaatcttcatatcctgctttgattgtctttctttatgttgagttagcttgcttacaggtagacagttcagagtatggcatctacttatcattggttgtttc--attgtgtgctgtagGAGGAATGATGTCACTCGCTGTCAAGTCTAAAACAGCTGATACGGTTAAGTGTGAAGTAGTTGATGGTGGGGAACTGAAATCAAGGCGCCACCTAAATGT
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0151g01100.t01 (Vitis vinifera), 3'ss of exon 1
ataatctgagagttttagaggaatttattaaattgttggatgaccaccaattttgattatctgtaaagatgattttaatctcttctgattgttatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT---------------------------------------------------------
|||||| | |||||| || ||| | ||| || | | | | | || |||||| | || ||||||||||| | ||||| || |||||||| || || |||||||| || |||| |||||||||||||| |||||||| |||||| ||| |||||
---------------------------gtaaattat--gatgact-----ttgtgaatga-tgtggaggt----tggagatatactacttgttaat---ggtggaatgatgtcattagctgtgaaatcaaagactaaggatttggttaagtgctaagTAATTGATGGTGGTGAGCTGAAATCAAGGCGTTGTTTGAATGTGCGTGGAAAAAGAGCAACTTTGCCTTCAATAACAGACAAAAACTGGGAAGATATCAA
upper sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 3
ataatctgagagttttagaggaatttattaaattgttggatgaccaccaattttgattatctgtaaagatgattttaa----tctcttctgattgttatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT
| ||| || | | | || ||| | || || | || ||| |||| |||||| | ||||| | | | |||||||| || | ||| ||||||||||| | | ||| || |||||| | || || |||||||| || |||| |||||||||||||| |||||||| |||||||| || |||||
gttttcttcaagcaattt--gcttataaaaaaaaaattcat-actggccatattgcttatttgtaaacaagatttaatgaattattttctgatt-ttgtgctagGTGGAATGATGTCATTAGTTGTGAAATCAAAGTCTAAGGATTTGGTTAAGTGCCAAGTAATTGATGGTGGTGAGCTGAAATCAAGGCGTCACTTGAATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaattttgattatctgtaaagatgattttaatctcttctgattgttatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT
ttctgat putative branch site (score: 3)
ttatttc putative PPT
taaagatgattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataatctgagagttttagaggaatttattaaattgttggatgaccaccaattttgattatctgtaaagatgattttaatctcttctgattgttatttcagGAGGAATGATGTCTCTTGCTGTTAAGTCAAAGACAAAAGACTTGGTTAAATGTGAAGTTATTGATGGTGGTGAACTGAAATCTAGGCGTCATTTAAATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - ttgttgg
- - - - - - - - - - - - - - - - - - - - tgaccac