Sequence
atgc intronic sequence ATGC exonic sequence...gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
Basic information
species | Glycine max |
transcript | GLYMA15G13580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g52940.1 (Oryza sativa), 3'ss of exon 2
gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| || | | ||| | | | || | |||| |||| || | |||| | || ||| | | | || |||||||| || ||||| || ||||| ||||| | ||||| || || ||||||||||||||||| || ||||| |||||||| || |||| ||||| || |
-----------gtgagtgcttacacttttagtgaccatgtgttgtgtaag-gtatatttgttt---gattcagcggtcatcttgctatttc---tttcagGTGGATACTATTTTAGACAAGGAAAATTTCAAGTTGGAGGACCTTCTTGATGAGGATGAAATAATCCAGGAGTGCAAAGCACTAAACACCCGCCTAATCA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
--------gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| | | || | | | |||| ||| || |||| | || | | || | || | || || ||| |||||||| || ||| | || |||||||| || || || || ||||| ||||| ||||||||||| |||||||| |||||||| || || | ||| || ||||
tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatg--ggaacatctctacctaacccgccta------actttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G806347_T01 (Zea mays), 3'ss of exon 1
gggggacta-gaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcga----ttttactgt--ttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
||| ||||| || | ||| | | | | ||||| || || || || ||||| | | || ||| ||| | || |||||||| || ||| |||| || || |||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| || ||| | || ||||
-----actgcaaatagcttgaaccatggaggcctttcgtttttttcttcctcatttattgttaaagagaggttcttaactgtgctaacttagtg-attttttt-cagGTGGATACAATTCTGGACAAAGAAAATTTTACATTGGAAGAACTTCTTGATGAGGATGAAATTATTCAGGAGTGCAAAGCACTGAACTCAAGACTCATAA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 1
gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatatt--gcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
|||| | | | | | | | | | ||| || | | | ||||| | || ||| |||| || |||||||| || ||| | || || || |||||||| ||||| ||||| ||||| |||||||||||||||||||| |||||||| |||||| || || ||||
-gggggcaatattttcggggccctgggcggccactcggctcgaccccccacaggtac-ggccctgtcttaattctgttaacttagtgctttattttttccagGTGGATACAATTCTTGACAAAGAAAATTTTACATTGGAAGAACTTCTTGACGAGGATGAAATTATTCAGGAGTGCAAAGCACTTAACTCACGACTCATAA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G096107_T01 (Zea mays), 3'ss of exon 2
gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| || | | || || || | | || | | | || | || || ||| | || ||| ||| || |||||||| || |||||||| ||||| ||||||| ||||| || || ||||||||||||||||| |||||||| |||||||| || || | ||| | || |
-----------gtgagtgcttgcagttcgatgttcat--ttattttttttctcctaa-gctacagttttttaaacattccttttatgtcttt-----cagGTGGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAGGATCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G000039_T01 (Zea mays), 3'ss of exon 2
gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattt---tactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
|| ||| || | || | | || | | | || |||| | |||| |||| |||| || ||| | || ||||| || || |||||||| ||||| ||||||| ||||| || ||||||||||||||||| |||||||| |||||||| || || | ||| | || |
---------------gtgagtgc--ttgcacttcgatgttcatgttttccctcctaa-ggtacaattatttgttaactgcacatttcgt-tatc-tctttcagGTTGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAATGTCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
gggggactagaataggttag--tttaatttaatttttaaaatgatatg-tagatacgtat------tggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| |||| ||| | | ||| | || || ||| | || | | | | | | || | | || ||| |||| | | || | |||||||| ||| | ||||||||||| || | ||| || || || || || ||||| ||||||||||||||||| ||||||||||| || || | || || |||
--------ataatatgttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgt-ttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgta---ttggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| |||| | | | | ||| | || |||| | | | | | || | | || || | | |||| | ||| | ||||||||||| || |||||||| ||||| ||||| |||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| | |||||||| |
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatat-gtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
upper sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S112_230V6.1 (Physcomitrella patens), 3'ss of exon 1
-gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
| || | | | || || | || | | ||||| || || |||| | | | || || | | ||| | | ||||||| || | | | || || || | || |||| || || || |||||||||||||| || |||||||||||||||||||| || ||||| || |
ctgcacgctgcagttgaatatttgtgtatattcgctttgctgataggtc-attgatattttcttgctattagtgctaagtagtggctgtctacttatgcagGTTGAGTCGGTGCTCGACAAAGATGTCTACACCCTGGAAGAGCTCCTGGATGAGGATGAAATCATCCAGGAATGCAAAGCTCTTAATAGCCGCCTCATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
attttactgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
gggggac
- - - - - - - - - - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg