Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaattt------cttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
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----------------------------------------------gttctaaaagcttgccaagg----aaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
upper sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 7
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
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--------------------------------------acttctagctgcaaattagttactatagtcattagttttgtgtatacttgcagttgaatacaaatcaatatattgtt-atatt-ttccttttcctatgcc----agTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAG
upper sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 5
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaatt--cattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
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---------------------------------------acttctagctgctattattgttactatagtcattattt-ttgtcttactttcagttgaatacaaataaatatattgtt-atatt-ttccttttcctatgcc----agTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG
upper sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaatttcctcatgcaacaaagacataagactggcat-gccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcag-atgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
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-----------------------------------cattacacgtcagcaaatgaaactt---gtggttaagataa-ctccaaaaaatgagatctaatttagtatgatt-tgctac--atg---tatgatgtctca-atgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAGMapped 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|226431382|gb|GO477718.1|GO477718EST: ATTGAGAAAGATGAAAGCCTGGATAAC TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: ATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST:
gi|89106387|gb|DY576604.1|DY576604EST: GCCTGGATAAG TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST:
gi|6526946|gb|AW216191.1|AW216191EST: GGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAG TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
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:
650GATTGAAGTTCCTGTTGGGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
411GATTGAAGTTCCTGTTGGGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
311GATTGAAGTTCCTGTTGGGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
1119GATTGAAGTTCCTGTTGGGAGAGGAAAACCACCTGTACTTATTGAGAAAGATGAAAGCCTGGATAAGgtaaatttcc ... tgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggacttgtgcagatgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
tactgat putative branch site (score: 1119)
tttcttgtgtctctt putative PPT
agatgattatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttcctcatgcaacaaagacataagactggcatgccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcagatgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA