Sequence
atgc intronic sequence ATGC exonic sequence...ttattagaacattgtgagagggattttgtgtcttaggtttagaatcatttattaatatttttcaggactactgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
Basic information
species | Glycine max |
transcript | GLYMA16G02770.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 12
ttattagaacattgtgagagggattttgtgtct-taggtttagaatcatttattaatatttttcagg-act--actgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
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-----gtaagtttccgattattcttctatttgaatagaatgaataccaat-gccattgatttccagttacttggtctatgctgaactgctaagtatctgtttagGTCAAGCTTTCGGAGAAGCTTTCACATGTACAGTCCCTCTGTGTACATGAGATGATAGTGAGGGCATTCAAGCATATCGTTCGCTCTGCAATTGCTGCTA
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 14
ttattagaacattgtgagagggattttgtgtcttag-gtttagaatcatttatt-aatatttttcaggactactgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
|| || || ||| | | | | |||| | | |||| || || | || | |||| | |||| | | |||||| ||||||||||| || | |||||||| ||||| || ||| |||||||||||||||| |||| ||||||| ||||| | ||| || ||||||||||
-------------gtaagttggctttcttaacctcgtgtttcttagaaactattcaagatgaattttgatcatccatat---cttttttatggtgacaatagGTGAAGCTTTCAGATAAATTGTCACATGTACAATCGCTGTGTGTTCATGAGATGATAGTAAGAGCCCTTAAGCATATCCTCCAGGCGGTGATTTCTGCTG
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0002g01140.t01 (Vitis vinifera), 3'ss of exon 5
ttattagaacattgtgagagggattttgtgtctta-ggtttagaatcatttattaatatttttcaggact--actgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
| || | | | | | | || ||| | || | || || | |||||| || | | || ||| ||| ||| || |||| || |||||||||||| | ||||| || || |||||||||||||||||||||||||| || |||||||||||||| ||| |
-ttttgaagcgtccatataatattgttcaaaattatgaaatattactatacatgggtttttttcccatctcaaataatgcttgttattt--tttctttaccagGTTAAACTTTCAGAAAAGTTATCACACGTGCAGTCACTTTGTATTCATGAGATGATAGTGCGGGCTTTTAAGCACATTCTGTAG----------------
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 14
ttattagaacattgtgagagggattttgtgtctta-ggtttagaatcatttattaatatttttcaggact--actgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
| || | | | | | | || ||| | || | || || | |||||| || | | || ||| ||| ||| || |||| || |||||||||||| | ||||| || || |||||||||||||||||||||||||| || |||||||||||||| |||| ||||||||| ||||||
-ttttgaagcgtccatataatattgttcaaaattatgaaatattactatacatgggtttttttcccatctcaaataatgcttggtattt--tttctttaccagGTTAAACTTTCAGAAAAGTTATCACACGTGCAGTCACTTTGTATTCATGAGATGATAGTGCGGGCTTTTAAGCACATTCTGCAGGCAGTAATAGCTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttattaatatttttcaggactactgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
tactgat putative branch site (score: 2)
tatttgccttttactt CT-rich tract
attaatatttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattagaacattgtgagagggattttgtgtcttaggtttagaatcatttattaatatttttcaggactactgatatttgccttttacttttcttgatagGTCAAGCTTTCAGAAAAGCTTTCACATGTCCAATCACTTTGTATTCATGAGATGATAGTTCGAGCTTTTAAGCACATCCTGCGGGCAGTAATTTCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - -gagaggg
- - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actactg