Sequence
atgc intronic sequence ATGC exonic sequencegtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 11
gtaccttttcatttctccgtagctcagcattaaccacctgt--tcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
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gtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcagGCTCAGCAATTGAATAAGGATATCTTCGAAACTATTTACTTTCATTCTCTGAAAGCTTCCGCTGAGCTTGCTGGTAAAGAAGGTCCCTATGAAACATATG
upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 11
gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatctt----ttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
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---gtaaataacatttatgggactgctttttcatctacaatttaagctagaggttcatcaatttg--atagttttcctggacatgggatgcagGCTCAGCAGTTGAACAAGGATATATTTGAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATATA
upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 13
gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
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-----------------------------------------------gttcatcaatttgatactttacat-tgacatgaggt--gcagGCTCAGCAGTTGAACAAGGATATATTTCAGACTATATACTATCATGCACTAAAAACTTCATCTGAATTGGCTGCAAAAGAAGGTCCCTATGAAACATTTA
upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 11
gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
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gtaaatct--acttctg---aggctgctgtta--tattcgttgtatt-tgtgcttcagtctaatagttcacttggat--attaatgcagGCTCAGCAGTTAAACCAGGAGATATTTGAGACTATATACTATCATGCTCTAAAAACTTCATGTGATTTGGCTGCAAAAGAAGGTCCCTATGAGACATATA
upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
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------gtagacttgttt-tgaattatgatcaatcttggaaaatataattttgttatctgttcttaagcagtttaatttgt-tactcagGCCCAACAACTGAATAAGGATATATTCGAAACCATATACTACCATGCACTCAAAGCATCTACAGAGCTTGCTGCAAGACTTGGCCCCTATGAAACCTATGMapped 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|211165343|gb|FL103231.1|FL103231EST: GCCTGGCAGATACTTTCATATTATTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|211165341|gb|FL103229.1|FL103229EST: GCCTGGCAGATACTTTCATATTATTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|32933128|gb|CF037940.1|CF037940EST: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|211102666|gb|FK948700.1|FK948700EST: GCCTGGCAGATACTTTTATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATRCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|33098100|gb|CF058060.1|CF058060EST: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|32931387|gb|CF036199.1|CF036199EST: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATAT-T-CGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|32930756|gb|CF035568.1|CF035568EST: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST:
gi|211165338|gb|FL103226.1|FL103226EST: GCCTGGCAGATACTTTTATATTACTGGGCATGCCGTTTGATTCACCAGAG GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
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),
49 (downstream exon)
Score:
523AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
113AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
97AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
Block sizes:
48 (upstream exon),
46 (downstream exon)
Score:
123AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
atgtaac putative branch site (score: 123)
ttttatcttttc putative PPT
ttttatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG