Sequence
atgc intronic sequence ATGC exonic sequence...tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
Basic information
species | Glycine max |
transcript | GLYMA09G39740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
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--------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagag---aacat-ctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
upper sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
||| | | | |||| || | || ||| || | | | | || || | || ||||| |||| ||||| ||||||||||| || || || || ||||||||||| ||||| |||||||| ||||||||||||| ||||||||| ||||| |||
----gtatttctcttttcttcttcttcctccatt---gttactctgtttttcgacaatgcttcattgttttaaaagaccacatcttttcttaac--acagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
upper sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
| || | | | ||||| | | ||| | ||| | | | | || |||| ||| | | | | | |||||||||| ||| ||||| ||||| || || | || |||||| | || ||||| ||||| |||||||||||||||||||||||||| ||||||||| |||
--------------gtgcactcatt--actcattt-tcttgttagatcttctatgatcatattatatcaa-----caatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
upper sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
----------------------tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
||| || ||| | | | | | |||| | | | || | ||| || | | || | | | ||||| |||| |||||||||| |||||| || |||||||| |||||||| ||||| || || ||||| || || |||||||| |||||||||||||||||||| |||||||||
gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatctacgtaaatttatgagata-taaca-agtgggttttactttg-----cagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
cgctaat putative branch site (score: 3)
ttttatttt putative PPT
aatatattttattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- tgatatg
- - - - - - - - -caatgaa
- - - - - - - - - - - - - - - - - tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgca