Sequence
atgc intronic sequence ATGC exonic sequencegttatctttaattctttgatcattctctttttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
Basic information
species | Glycine max |
transcript | GLYMA11G16460.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 12
gttatctttaattctttgatcattctctttttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
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-----gtttgttttgttatctgttgtatttttc----taaatctatcatttgtgaactttaaagtgtaaattttgatcgc-agACAATTATTTCTGGGATGGGTGAGCTGCATTTGGATATCTATGTTGAACGCATCAGGAGAGAGTACAAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 12
------------gttatctttaattctttg-atcattctctttttaagtacaatattattgttcgt--atgttgatattagtaaacttctgtggt-tagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
||| |||| | | | |||||| | | ||| |||| | | ||| | | | | | | | ||| |||| || |||||||| ||||||||| ||||||| || ||||||||||||||||| | ||||| ||||||
gtatcatctaaaaactcttttgcttctcagcacctctctcttaattcaccccatagtatttaacattgatgattcttccatttatccttcatgggacagACGATTATTTCTGGTATGGGGGAATTGCATTTGGACATCTATGTTGAACGCATGCGAAGAGAATATAAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 12
------------gttatctttaattctttg-atcattctcttt-ttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggt----tagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
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gtatcatctaaaaactcttttgcttctcagcaccactctcttaattcaccccattagtatttaacat-tgaggattcttccatttatccgtaatgggacagACGATTATTTCTGGTATGGGGGAATTGCATTTGGACATCTATGTTGAACGCATGCGGAGAGAATATAAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 12
gttatcttta----attctttgatcattctctttttaagtacaa-tattattgttcgtatgt-tgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
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gtttaatttatgacatgcatttcacacattccttagaggaagaagttttatcatgcctaaccatgacatcaaaatgctttcttgtgcagACAATTATTTCTGGAATGGGAGAGCTGCATTTGGACATTTACGTTGAACGCATTCGGAGGGAGTATAAG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S100_33V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------gttatctttaattctttgatcattctctttttaagtacaatattattgttc----gtatgttgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
|| |||||||| | | || | | |||| || || | || | || || || |||| |||| || ||||| |||||||| || |||||| ||||||||||||| ||||||||| | | || || |||
actgtgcagttggttgattttactttaattttgtagaagttgtgatag-aagttcagcgg-atcgatctgaagcgcagggacgggggttgggttttgtg--cagACCATTATTTCGGGAATGGGAGAGCTGCATCTAGATATCTATGTGGAACGCATTCGTCGTGAATACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
tgttgat putative branch site (score: 4)
cttctgt putative PPT
tacaatattattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatctttaattctttgatcattctctttttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggttagACAATCATTTCTGGAATGGGGGAACTGCATTTAGATATCTATGTTGAACGCATTAGGAGAGAGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA