Sequence
atgc intronic sequence ATGC exonic sequenceTTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgacccgttttcctaaagtgttctttacagtacacacttttcctcttctgcag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 10
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgac-------ccgttttcctaaagtgttctttacagtacacacttttcctcttctgcag
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TTACACAAGAACAACTTGATCGTGCTAAAGAGGCTACCAAGTCTTCAGTTCTGATGGACTTGGAATCAAGAgtatgttgttcttactcctgatcaagttccaatcgcatgaatttcatgcttcttccctgaaatgtttttttaattgtac--ttcctccttatcgcag
upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G36040.1 (Glycine max), 5'ss of exon 10
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgacccgttttcctaaagtgttctttacagtacacacttttcctcttctgcag-----------------------------------------------------
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TTGACCAGGTACAGCTGGATCGAGCCAAACAGGCTACCAAATCTGCAATTTTGATGAATTTGGAATCAAGAgta-agtaaatacatctcaaatgaaattttatatggaaattacaatggca-aaaatttatttttcaattttcattcagtttttcttattgtgctttttttttggtaactatctaatcactactgaactttatgtttttttcag
upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 10
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgaccc---gttttcctaaagtgttctttacagtacacacttttcc-tcttctgcag--------------------------
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TTAACCAGGCACATCTTGATCGTGCCAAGGCAGCCACAAAATCTGCAGTTCTGATGAATTTGGAATCTCGGgtatatttttaactctcgcaccctctacttacataaaaatacttaaatgttgccaatttgtttaacttgatccaaaccattatatgttatgaatgtgttcaaacggttttcctgtgccag
upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 5'ss of exon 9
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaa--atcctaactgtatgacccgttttcctaaagtgttctttacagtacacacttttcctcttctgcag-------------
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TTGACCAGGTACAACTTACTCGTGCCAAAGAGGCAACTAAATCTGCCGTTCTGATGAATCTGGAATCAAGAgtatgcttctctctctctttccccaccaccccaacc-tgcaacccctttgggtttggtctttgctg-agttttcttttgttatggcttacacttgtttgttgtag
upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 5'ss of exon 10
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgacccgttttcctaaagtgttctttacagtacacacttttcctct--tctgcag-------------
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TTGACCAGGTACAGCTTACTCGTGCCAAAGAGGCAACTAAATCTGCCGTTCTGATGAATCTGGAATCAAGAgtatgcttctctctctctctttccccaccaccccaacctgcaccccctttgggtttggtctttgctgagttttcttttgttatggcttacacttgtttgttgtagMapped 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|40333865|gb|CK367935.1|CK367935EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|89758987|gb|DY687957.1|DY687957EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|30031571|gb|CB833422.1|CB833422EST: CCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: CCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|71438038|gb|DR819088.1|DR819088EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|32863948|gb|CF003630.1|CF003630EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|211146232|gb|FL303723.1|FL303723EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
EST:
gi|40336960|gb|CK371030.1|CK371030EST: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGG TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
genomic: GTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
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:
146TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
119TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
111TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
204TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgtt ... tcttctgcagTCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTACACAAGAACAACTTGATCGTGCTAAAGAGGCAACCAAATCTGCAGTTCTGATGAACTTGGAATCAAGGgtacactgttcttgctcctgatcaaatcctaactgtatgacccgttttcctaaagtgttctttacagtacacacttttcctcttctgcag
- - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - CTGCAG