Sequence
atgc intronic sequence ATGC exonic sequence...cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 6
cttcatttagcacataagaacttatttaaat-gtgttgggcacttaatcaccaa-aacataatagaaattg---------------ccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
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--gtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAACCTTTCCGCACCTCAAACATTCCGATCCAAGGAGATCTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 3
-cttcatttagcacataagaacttatttaaatgtg-ttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctt--tcattcatg-cagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
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gattttttgtatgcttaaactttaattaaaataaaattgaagaacgtgttggggagaagtac-----attgatgatgttttaattgtctgggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATCTGGGCAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCTAAGGAAATCTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------cttcattta-gcacataagaacttatttaaatgtgttggg-cacttaatcaccaaaacataatagaaattgccaagggcacatttccctt--tcattcatg-cagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
|||||| | ||| | ||| |||| | | | | | ||| || | | | | || ||| | || || ||||| || || || ||||| |||||||| ||||||||||| || | |||||| || || ||||||||||| ||| | || ||||| || ||||||||||| |
gtacaacttttgttgttttgcttactaatactattgctatatcacgtgtgctactacttttattggttaataataaggacagagtatcatttgtatgcttaaactttaattaaaataaaataaaataatgtgttggctaaaaatggagaagtaaattgatgttttaattgtcttggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATTTGGGAAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCGAAGGAAATTTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
---cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
||| || | | | | | || |||||| | || | | | | || | | | |||||| |||| || || | |||| || |||||||| || |||||||| | || |||||||||| ||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
gtacttaatcctaaata-agtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgc---------atttatct---atatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 6
cttcatttagc--acataagaacttatttaaatgtgttgg-gcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
|| |||| | | || || ||| | |||| | | || | || || | | | | | | ||| ||| |||| || || |||||||||||||| ||||||||||||||||| | ||||| || || || || || || ||||| || |||||||||||||| ||||| |
gtttgtttaacttgcgtatcaagttactctttcttgttactgaaaatatttgtcacaagact-ttggtttcattgattgtgtgtttttgttt-------atagCCTACTTCAATTGTGAGCTACAATCACTTGGGAAACAACGATGGAATGAATCTCTCAGCTCCACAGACTTTCAGATCTAAGGAGATCTCCAAAAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 4
cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
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-----gtaatagaattaaagcttgtttat-caagtaacctaacttgcttctcttctgttagtgaaggaactaagaatggattttgtg---------gcagCCTACTTCGATTGTGAGCTATAATCATTTGGGAAACAACGACGGGATGAACCTCTCAGCGCCACAGACTTTCCGCTCTAAGGAGATTTCAAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 6
------------cttcatttagcacataagaactta----tttaaatgtgttgggcacttaatcaccaaaacata-atagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
||||| | || ||| |||||| | | | | | | || || | | || | | | || | | | ||||| || || ||||||||||| ||||| ||||||||||||| | |||||| |||||||| |||||||| ||| | ||||||||||||||||||||||| |
gtatatcatttttagcatttcctctgttgaaatttagaattttaaagtaaataagtatgcatgtataggattatgtatgaataatgatattgaaagatgatgatggtggtga--cagCCAACATCCATTGTGAGCTATAACCATCTGGGAAACAACGATGGCATGAATCTGTCTGCTCCTCAAACCTTCCGCTCCAAGGAGATCTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcatt-catgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
|| ||| | || ||| | || | | || | | || | | || | || || || | ||| ||||||||||| |||||||||||||| || |||||||||||||| | ||||||| |||| || ||||| || || | ||||||||||||||||| ||||| |
gtgattcctaagcatctcgtttggttcactggaagt-atccggttctctttaaatcgttttctatggtttgtcac-gatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------cttcatttagcacataagaactt-----atttaaatgtgttgggcacttaa---------tcaccaaaacataatagaaattgccaagg----gcac--atttccctttcattcatg----cagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
| |||| | | || ||| | ||||| | ||| || | | || ||| | || | |||| | | | | || || ||||| || || ||||| ||||||||||| ||||| |||||||| | |||||| |||| ||||||||||||||| | ||||||||||||||||||||||| |
gtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAACTTGTCCGCCCCTCAAACATTCCGTTCCAAGGAGATCTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 6
cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
||| | | | || || | | || ||| ||| ||||| ||||| ||||| |||||||| || | || ||||| || | ||||| || ||||| |||||||||||||| |||||||| |||||||||||||| |
------------------------------------------gtaaaatctcgtttttctcgtatttttccgactctaaatccgtcttgtcttc---cagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCTCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG
upper sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 6
cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
||| | | | || || | | || ||| ||| ||||| ||||| ||||| |||||||| || | || ||||| || | ||||| || ||||| || ||||||||||| |||||||| |||||||||||||| |
------------------------------------------gtaaaatctcgtttttctcgtatttttccgactctaaatccgtcttgtcttc---cagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCGCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
acttaat putative branch site (score: 4)
catttccctttcattc putative PPT
aaaacataatagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcatttagcacataagaacttatttaaatgtgttgggcacttaatcaccaaaacataatagaaattgccaagggcacatttccctttcattcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGACATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-ttcattt
- - - - -gcacata
- - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccaag