Sequence
atgc intronic sequence ATGC exonic sequenceTGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaattaacttgctgaatgtatggtctataaataccaaaggacttatagactaacttggctttatccccag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G167886_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 4
TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaattaacttgctgaatgtatggtctataaataccaaaggacttatagactaacttggctttatccccag
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TGCATCGGTGGTCTGCCAGGTATTGTCTTCTCCTGCCTGCTCCAAGGTCAACCATTGCAGCTGCATTCAGTCCGGATGGGAGAACACTTGCATCCACACAgtaagctaaaggatatgctgaatatatgttctg--aacggaaaaaaactta--gactaactacacttt-tctctag
upper sequence: GRMZM2G167886_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G35370.3 (Glycine max), 5'ss of exon 3
TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaattaacttgctgaatgtatggtctataaat---accaaaggacttata-gactaa--cttg----gctttatccccag
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TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagtt--ttaactagttgatctcctctttactaatttgaatctatgaacttttgtgattgaatcttgttatgtgttatgtgcag
upper sequence: GRMZM2G167886_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G32620.2 (Glycine max), 5'ss of exon 3
TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaattaacttgctgaatgtatggtctataaat---accaaaggactt-atagactaacttggctttatccccag-----
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TGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAAGTTCTTGCCTCCACACAgtaagtt--ttaactagttgatctcctctttactaatttgaatctatgaactttgtgatcggatcttgttatgtgctatgtgcagMapped 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|18384883|gb|BM418082.1|BM418082EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA TGGTGACCATACTGCCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST:
gi|18385319|gb|BM418518.1|BM418518EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA TGGTGACCATACTGTCCAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST:
gi|18384882|gb|BM418081.1|BM418081EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST:
gi|76015702|gb|DT942872.1|DT942872EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA G
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccag-
EST:
gi|76015702|gb|DT942872.1|DT942872EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA G
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccag-
EST:
gi|22489334|gb|BU049257.1|BU049257EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST:
gi|87298785|gb|DY470788.1|DY470788EST: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
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:
14 (upstream exon),
44 (downstream exon)
Score:
13TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
Block sizes:
36 (upstream exon),
41 (downstream exon)
Score:
13TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
Block sizes:
45 (upstream exon),
48 (downstream exon)
Score:
12TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
Block sizes:
34 (upstream exon),
49 (downstream exon)
Score:
16TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaattaacttgctgaatgtatggtctataaataccaaaggacttatagactaacttggctttatccccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG