Sequence
atgc intronic sequence ATGC exonic sequencegtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
gtaatc--cgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|||||| |||| | |||| ||| | ||| | |||| | || | | | || | || | | || | | | ||||||||| |||||||| ||||||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| |||||||| ||||
gtaatccccgatatc-ccgattcgcg-------ccctcgctcgattgtcgtttccgcaccccc--------ttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
--gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|| | || | | | | | | |||| | | || ||| | ||| | | || | | |||| || ||||||| |||||||||||||| || || ||||||||||| ||||||| |||||||| ||||| ||||| ||||| || |||||||| || ||||
ttctagctattcttttttgatgtattcataatagttggtttcattt-ttaccaattgacttaca-agacactaagtaagtgtttgcttcttttattttg--tagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 1
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcgg--agaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
| | | || || || | | | ||| | | || | || | || ||| | | ||| ||||||| || |||||||||||||| ||||||||||| || |||||| | |||||| || || ||||||||||| || |||||||| || ||||
------------------------gtacgcgcttgttgttgttgttgattaatgcatttggtgttatgatgatgaaactaattgattgat-tgactgtg--tagATGCTGACATGGAGGACTACGGTTTCGAGTACTCCGATGAGGAGGAAGTGGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcg-----gagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
| | | | || || | ||||| || || || | | || | | | || | | || | |||||| || ||||||| |||||||||||||| || || ||||||||||| ||||||| ||||| |||||||| ||||| ||||| || |||||||| || ||||
----tttgctagttatt-cttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctg--tagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 1
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
| | | | || || | ||||| | | || | | ||| | || ||||| || ||| ||||||| || ||||||||||| || ||||||||||| || ||||||| || ||||| || || ||||||||||| || |||||||| || ||||
--------gtacgcgcttgttgttattgttgttgttgattat--gcatttggtgttacgatgatgaaactaattgtttgattg--------attgtg--tagATGCTGACATGGAGGACTATGGCTTCGAGTACTCTGATGAGGAGCAAGAAGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------gtaatccgatccctc----cgactcgtgggctaaattctctattatttg-tggcttgttctcttgcgga--gaattttttttcttgatcatggatgtta--tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
||||| | | | | || || || ||| | ||| | | || || | || | |||| ||||| || | | | || ||||||| || ||||||||||| || |||||||| || || ||||||| ||||| || ||||| || || |||||||||||||| ||||||||||
gtcttgttcttgttttgctatgtctaatcttctactctgaaacaatctagggttcgaaagttcccgaattcgactacttactttgttacgaatcgatagtgttttattgatttgggttttcgatttttgtgtagATGCTGACATGGAGGACTATGGATTCGAGTATTCTGATGAGGAGCAAGAGGAACAAGATGTTGACATTGAGAACCAGTATTATAACTCTAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttct----tgatcatggatgttatggtgat---tagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
| ||| | | | |||||| || || ||| | | || | | ||| || | |||| | || | ||| | ||||||| || |||||||| || || || ||||||||||| |||||||| |||||||||||||| ||||| ||||| || |||||||| |||||||
-------gtatccttgaaagtgcaaattct-ttctctcatacagatg-cttaatttattctgtaatggtttgttaataaaatgatttggaattctttggcattctgtagATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaatccgatccctccgactcgtgggctaaattctctattatttgtg-gcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|| | || | | | | | | | | || || || | | | | | || | ||| | | |||||||| || | ||||||||||||||| || || || || ||||| || || |||||||| || ||||| ||||| || |||||||| ||||| ||||| ||||||
gctagtacgtgacaaggatatacttgaatctgtgcgtgacggttattgtactaggtattgtaagtagctcatggttttcttttgatggatgtcattgc----agATGCGGATATGGAAGATTATGGCTTTGAGTATTCTGATGAGGAGCCTGAAGAGCAAGATGTTGACATCGAGAATCAGTACTACAATACTAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatccgatccc-tccgactcgtgggctaaattctctat-tatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|| | | || | ||| | | | || ||| ||| | || ||| | || | | ||| || || | | |||||| || ||||| || || ||||| ||||| || ||||||||||| || ||||| ||||||||||| ||||| |||||||| || | ||||
-tattatacttgagtctggctctttacgatgaggaacgatatatatgtagagtgaatgtatgcattagttaaccgttatc--ttttggctgacctgatcac-agATGCAGACATGGAAGATTATGGGTTTGAGTATTCTGACGAGGAGCCTGAAGAGCAAGATGTCGATATTGAGAATCAGTATTATAATACCAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatccgatccctccgactcg-tgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|||| | ||| | | | | | || | ||| | | ||| ||| | || | | || | |||||| || ||||| || || ||||||||||| || |||||||| || |||||||| ||||| ||||| ||||| || ||||| || | ||||
---tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 1
gtaatccgatccctccgactcgtgg-gctaaattctctattatttgtggcttgttctcttg------cggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
| | || || || || | ||| | | |||| | ||| | |||| | || | | || | | | | | ||||| |||| ||||| ||||| || || || || |||||||| || || || || |||||||| ||||||||||||||||| ||||| |||||||||||||
---gtaagctctcttcgtagcgcagcgctcactagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG
upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 1
gtaa--tccgatccctccgactcgtgggctaaattctctattatttgtggcttgttc--tcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
|||| || || || || |||| || || | | | | |||| || | | || | | | | | ||||| |||| ||||| ||||| || || || || |||||||| || || || || |||||||| ||||||||||||||||| ||||| |||||||||||||
gtaagctctcttcgtagcgcagcgctcgctagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|31664621|gb|CD573554.1|CD573554EST: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAG ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST:
gi|29946668|gb|CB816265.1|CB816265EST: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAG ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST:
gi|211131141|gb|FL290028.1|FL290028EST: CTAGCGCTCGTGTCCCCGTTTTGCTCCCGTCGCCGCTACCATGGGCTCAG ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST:
gi|29946544|gb|CB816202.1|CB816202EST: CTAGCGCTCG-GTCCCCGTTTAGCT-CCGTCGCCGCTACCATGGGCTCAG ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST:
gi|211131142|gb|FL290029.1|FL290029EST: CTAGCGCTCGTGTCCCCGTTTTGCTCCCGTCGCCGCTACCATGGGCTCAG ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
156GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
Block sizes:
46 (upstream exon),
49 (downstream exon)
Score:
82GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
55GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
68GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
tcttgat putative branch site (score: 68)
aattttttttcttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG