Sequence
atgc intronic sequence ATGC exonic sequenceGATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G103897_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g45100.1 (Oryza sativa), 5'ss of exon 10
GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagt-tgtcttt----------agt-----atgaccaaaggaaataaat---------tcaaa---aaaaaattaca----agtg-----tcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactct-gacag
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GATATGGGTATTGATTGGCGAATGGGAGCTGAATGGTTTGAAACATGCCTATTGGATTATGACCCAGCTTCAAATTATGGTAATTGGACATATGGAGCAGgttagtgtttctttcctcatatacagttacttattcttgaaagcattgtataatcattagtcaaagcaaacaaatgacacaaaagtgggagctcatttacatatcatgccagactctga--gactgaactgctactactgtaatcttgacag
upper sequence: GRMZM2G103897_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA04G07870.2 (Glycine max), 5'ss of exon 11
GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgt---tagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacag
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GATATGGGCATTGATTGGCGCATGGGAGCAGAATGGTTTGAGACATGTCTTTTGGATTATGATCCATGTTCTAATTATGGAAACTGGACTTATGGATCAGgtaactaactatatttgg-ataactatgctagctaa-tcaactaatgcactactccgcaagattgcatgcagaaataagcctgcgtgtaccacactatttat---------------
upper sequence: GRMZM2G103897_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT5G24850.1 (Arabidopsis thaliana), 5'ss of exon 10
GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagact--ggaactgaatgaaatgtttctggtgtactctgacag
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GACATGGGGTTGGATTGGCGTATGGGTGCAGAATGGTTTGAGACATGTCTATTAGACTATGATCCTTGTTCTAATTATGGAAACTGGACCTATGGAGCAGgtaagtactactca-tgacacagtttgtgacttgtggttttcaaattcaacattgagaatgagattgaaatggaaactttatagatggttgaaatctgtttttcttaccattgaag
upper sequence: GRMZM2G103897_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g02670.t01 (Vitis vinifera), 5'ss of exon 11
GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtctt-----tagtatgaccaaaggaaataa-attcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacag
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GACATGGGCATTGACTGGCGTATGGGAGCTGAATGGTTTGAGACTTGCCTCCTCGATTACGACCCTTGTTCCAATTATGGAAATTGGACCTATGGAGCAGgtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcat-ctatatatgcattttaatatcctatcctgttttattagMapped 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|76283830|gb|DV023398.1|DV023398EST: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST:
gi|32909346|gb|CF014158.1|CF014158EST: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAG-TATCCCAAAACAA
EST:
gi|110957435|gb|EE177487.1|EE177487EST: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST:
gi|148999289|gb|EE036219.2|EE036219EST: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST:
gi|13149731|gb|BG320053.1|BG320053EST: ATTGGATTATGACCCAGCTTCGAATTWTGGCAATTGGACATWTGGVGCRG GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
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 3 RNA-Seq libraries.
Block sizes:
42 (upstream exon),
48 (downstream exon)
Score:
3GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
Block sizes:
19 (upstream exon),
31 (downstream exon)
Score:
2GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
Block sizes:
15 (upstream exon),
35 (downstream exon)
Score:
3GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG