Sequence
atgc intronic sequence ATGC exonic sequenceAGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatcta-attgtag
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AGTTGATGTGTGGAGTTGTGGTGTTATTCTTTATGCTCTTCTTTGTGGTACCCTTCCATTTGATGACGAGAATATTCCCAACCTTTTTAAGAAAATAAAGgttagcaaagatgtgatatatcctac-tgataaaggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctag
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtga-gcta---taatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag----
||| || |||||||||||||| || ||| | ||||| |||||||||||||| || || ||||| ||||| ||||||||||| || ||||||||||||||||| | || |||| | | | |||| | | || | | || || || | | | || | | ||||| |
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaa-acatcccaggccttggacatgtggataattttccagct
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag---------
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AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgtactatttttcttaatttaattattattatatttcctttttctttttatgggtttcaaaggactgatagttaaatttcctacc--actgtcgtgtcaaatt
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtg-----agctataatctcagtgattt---tacctgaaaaagattcctttatat---tttatttttaatatgctcaataaattctttttatatctaattgtag
||| || |||||||||||||| || ||| | ||||| ||||||||||||||||| || ||||| ||||| || |||||||| || ||||||||||||||||| | |||| | | | |||| || |||| | | || | | | ||| || || ||| || || ||| ||||||
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatgttaattttatttatttaattaactgagtgatcagctgttgtctacatatatattaaaactgcccag-gccttggacatatggctaattt---
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttattttta-atatgctcaataaattct-----ttttatatctaattgtag
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AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagct--aaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttag
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgag--ctataatctcagtgattt----tacctgaa--aaagattc--ctttatattttatttttaatatgctcaataaatt-----ctttttatatctaattgtag--------
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AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag---------
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GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgt-atttctaaatttacttcactaacttttagcatgtgccagcttagctggatctgcat-tgctcttttttgtccttttactttttatttttttgtttagaa
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 5'ss of exon 4
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgag-ctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag-------
|| || || ||||||||||| |||||||| ||||||||| | ||||| || | || |||||||| || || |||||||| || || |||||||| ||||| || | | || | | | || || | | | | | | | || ||| | || || |
GGTGGATGTGTGGAGCTGTGGCGTTATTCTGTATGCTCTTTTGTGTGGTTCTTTACCCTTTGACGACGAAAACATTCCAAATCTGTTTAAGAAAATCAAGgttagattgttggttcggcgtgtctagctatttgtttcgtgtctggtaacagcgctgcagtcgagtattgtgtttctttca-gtccgcttagaaccgcgta
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 5'ss of exon 4
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata-atctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattcttttta--tatctaa-ttgtag-----
|| ||||||||||||||||| |||||||| |||||||| | |||||| | | || || ||||| || |||||||| || | || | |||||| ||||| | | | | | | || ||| ||| | | | ||| | || | || || | || | | ||| ||||
GGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACGAAAATATTCCGAATTTGTTTAGGAAAATCAAGgtcggttgagtagtttgtttgtattttctgtctc--attgcctcctgtttagccactccagtgtctacgaatttgtcttgaactgtctggcttgttcatctt
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 4
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatat-tttatttttaatatgctcaataaattctttttatatctaattgtag
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AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtgaatcagtcagacaacaagaagtcttaaatgttttttcttttcttgtttattcccag-----------------------------------
upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 4
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag
||| ||||| ||||||||||| || || || || || ||||| ||||||| || || |||||||| || || |||||||| || ||||||||||| ||||||| | || | | | || || ||| | |||||| |
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtgaatcagtcagacaacaagaagtcttaaatgttttttttttcttgtttattcccag-----------------------------------Mapped 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|211517180|gb|FL332457.1|FL332457EST: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST:
gi|149013919|gb|EE043417.2|EE043417EST: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG GGTGGAATATATATCCTTTCCTAGTCATTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTT-CCTAGTCATTTG
EST:
gi|148954916|gb|EC900404.2|EC900404EST: TCTCCCATTTGACGATGAGAATATTCCAAACCTTTTNCA-GAAAATAAAG GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: TCTCCCATTTGACGATGAGAATATTCCAAACCTTTT-CAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST:
gi|9254260|gb|BE344728.1|BE344728EST: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST:
gi|31352455|gb|CD436812.1|CD436812EST: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
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:
48 (upstream exon),
46 (downstream exon)
Score:
212AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
Block sizes:
48 (upstream exon),
46 (downstream exon)
Score:
179AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
259AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
139AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA