Sequence
atgc intronic sequence ATGC exonic sequencegttagctatcataggtgataaaataggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
----gttagctatcataggtgataaaataggcctagcaagactgc-tctctacttatagaagtgttaccaaa-actaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
||| ||| | | | | ||| || || | | |||| |||| ||| | ||| | ||| | ||||| ||| ||| || |||||||||||||||||| |||||||| || || ||||| |||||||||||||||| || |||||||||||||||| ||||||||||||||||||
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttt-tccatgtgtcct-ctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 16
----gttagctatcataggtgataaaataggcctagcaagactgc-tctctacttatagaagtgttacc-aaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA--------
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gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttt-tccatgtgtcct-ctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAGTACGCAA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 19
gttagctatcataggtgataaaataggccta-gcaagactgctctctactt----atagaagtgttaccaaaactaacttgtttctcctcatgttctt---ctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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gttag-tgtcataattaagtttatggttgtgtacattcatgctatttatttcacaagaaataggttgacaaatgtacacattttgacttactatctatatgttagATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 24
gttagctatcataggtgataaaataggcctagcaagac-tgctctctactt----atagaagtgttaccaaaactaacttgtttctcctcatgttctt---ctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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gttag-tgtcatacttaagtttatggttgtgtacagtcatgctatttatttcacgagaaataggttgacaaatgtacacattttgacttactatctataagttagATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATG----------------------------------------------
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
gttag--ctatcat-aggtgataaaata-ggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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gttagtgccatccttaagtcaggaaatatggattgacaaaagtatacattatt------agtgctcctgcactta------ctatctatatgt-----tagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
gttagctatcataggtga---taaaatag-gcctagcaagactgctctctacttatagaa-gtgttaccaaaacta-ac-ttgtttctcctcatgt-tcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA-
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-ttag-tgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
gttagctatcataggtgataaaataggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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gttag-tgtcatccttaattcaggaaatatggattgactaaagtatacgt-tattagtgct-cctgcacttac---tatctatatatgt-----tagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 18
gttagctatcataggtgataaaataggcctagcaagactgctctctacttatagaa-gtgttaccaaaactaacttgtttctcctcatgttcttct-agATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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gttggtgtttacctactgtccga-atgtcttctga-----ctcttgaggtgtataatattttgttgcgaggaaatcgatttctcatattttcatcttagGTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
gttagctatcataggtgataaaata----ggcctagcaagactgctctctacttatagaagtgttaccaaaactaact-tgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
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--tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttgtgtggaaatgagtatagaaaattctataacttttttacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAMapped 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|84980594|gb|DW530943.1|DW530943EST: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
genomic: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
EST:
gi|211189269|gb|FL030572.1|FL030572EST: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
genomic: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
EST:
gi|67015674|gb|CO444423.1|CO444423EST: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
genomic: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
EST:
gi|67010650|gb|CO439399.1|CO439399EST: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
genomic: CACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATG
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),
49 (downstream exon)
Score:
87ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
95ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
75ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
179ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAGgttagctatc ... gttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
aactaac putative branch site (score: 179)
cttgtttctcctcatg CT-rich tract
ttatagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctatcataggtgataaaataggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA