Sequence
atgc intronic sequence ATGC exonic sequenceATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct----
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ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgatttt----ccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatc-atgacattttatattaaa---aaatccccctgatcactctgtcactcagaattttgttcagc---tgtgggtgtgtgttggtgct------------------------------------
||||||||||| || ||||||||||| |||||||| || |||||||||||||| || || ||||| ||||| | | || || || |||||||| || | || ||| | |||| || || |||| | || | | || ||||| | | ||| | || |
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgtaatctgtcttatttccagttgaatgcaaatggtac--attagatataaaagcaagtgcttgttgggagcacaatgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 30
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct-----------------------------------------------------
||||||||||| || ||||||||||| ||||| || || |||||||||| |||||| || ||||| ||||| | | || || || || ||||| || | ||| || || | || | | ||| | ||| | || | | | || | || | | ||| || |
ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGAgtatgtca-caaacttgtaatttgtc-ttatttccagttgaatgctactggtacatcagataaaaaaaaccagtgcgtggtgggagcacgtgctgtttaaaaatgttttaaacacttttgttattttattttattttgccttttctattgcag
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcag-aattttgttcagctgtgggtgtgtgttggtgct----------------------------------------------------------------
|||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| ||||| ||||||| | || || || |||||||| || ||| || | | | |||| || || | | | | || || | || | || | | ||||| |
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgtaatttctc-tcttat-ttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 21
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgt---gaattcactgatatcatgacattt------tatat-taaaaaatccccctgatcactctgtcactca----gaattttgttcagctgtgggtgtgtgttggtgct-------------------------------------------------
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-TACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAGtatgttgcaaacttgtaatttctctcttatttgcaagttgtatgcaactaatatgtctgataataaagaagcacaatgtgaaacttcttttggttttggggtaagaagatgctgtttaaattccgtaattattatttccctcccctcttattttgttacaga
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 25
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATA-CGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct
|||||||||||||| ||||||||||| || || ||||| |||||||| |||||||| || ||||| ||||||| | || || || |||||||| || ||| || | | | |||| || || | | | | || ||
ATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGgtatgacataacgcagaaatcaagaaaaacatgccagaggagtatgagtatgtttgcagacttgtaatttctc-tcttat-ttgcaagttgaatgcaactaatatggcag-------------------------------------
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 19
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctg------atcactctgt---------------cactcagaattttgt---tcagctgtgggtgtgtgttggtgct-
| ||||||||||| || || |||||||||||||| || ||||||||||||||||| || || ||||||| | | || |||||||| ||||| |||| || | | ||| | || | || | ||||| | || ||| | || | |||||| || | | ||| || |||| | | |||
GTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGAgtaagtgacttgatcaa-atccgtatatgtaatgtaaaaaagtgttactagcagctatcccctcgtagaacagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgcag
upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 19
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgata--tcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct---
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ATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcattttttatttgtttaagaaatttt-catgatgtaatttttct--tccatgcat-acacatgatgatagcttattagacatacttgtca-tattacaMapped 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|78022287|gb|DV490674.1|DV490674EST: GAAAAGTAAACCTGAAGAATATGA ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST:
gi|84980594|gb|DW530943.1|DW530943EST: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST:
gi|78021450|gb|DV489837.1|DV489837EST: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST:
gi|67015674|gb|CO444423.1|CO444423EST: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
EST:
gi|67010650|gb|CO439399.1|CO439399EST: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA ATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAAGAGA-TCCTA
genomic: GATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTA
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:
49 (upstream exon),
45 (downstream exon)
Score:
86ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
Block sizes:
47 (upstream exon),
45 (downstream exon)
Score:
107ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
131ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
385ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaat ... accttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaatc