Sequence
atgc intronic sequence ATGC exonic sequenceGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttccatcattgtccacctctttatgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 22
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttcc----atcattgtccacctctttatgaaataagacgttttcaataataaaactattttaat-gttactcttcaaatgtcgccttctttttag
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GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatattattattttccttgcttcatcaaaattaggtattaagagtaaacaaattcaaaaagagaattggctattcttgacataat-----
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtc--aatttccatcattgtccacctctttatgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag----
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GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgcta---gataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA03G27600.1 (Glycine max), 5'ss of exon 22
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtc--aatttccatcattgtccacctctttatgaaataagacgttttcaataataaaactatttt----aatgttactcttcaaatgtcgcct----tctttttag
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GACTTGTTAGCATTGAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAACGACCCTACGAATCCGAAGCACTATTGGAGATACCgtgagtcttaagctttgtctcagttaactacgctagataatctattactattgattattgaaccaccttttggaaaattatgatctaagtgtgctttggactgttgtcag
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT2G40840.1 (Arabidopsis thaliana), 5'ss of exon 22
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttccatca--ttgtccacctctttatgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag
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GATATGATGGCTCTGAAAGAAGAGTACACTACTCGTCCTGCAACAGAGGAGACAATCAATGATCCAACAAACCCCAAACACTACTGGAGATACCgtaagt-atttactactaactaacacacaaccctaagaactataccagttttaac--ttagactgtttt----ttgtgcatatag-----------------
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 5'ss of exon 21
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagt-caatttccatcattgtcc---acctctttatgaa---ata-agacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag
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GACTTGCTAGCACTGAAAAAAGAATACACAACACGCCCTGCAGCAGAGGAGACAATTAATGATCCCACAAATCCAAAGCACTATTGGCGATACCgtatgtacaaattttaatattttactcaactgccgtgtgcacgcatgcaaacgtgcttagacatcaaattatcttcctgttttatatcatgtgtgttcac--------
upper sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
lower sequence: PP1S253_27V6.1 (Physcomitrella patens), 5'ss of exon 14
------GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttccatcattgtccacctcttta----tgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag
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CTACAGGATCTTATGGCACTGAAAGATGAGTATGCCAAGCGACCAGCCAACGAAGAGACTATCAATGACCCCACCAACCCAAGACACTATTGGCGATTCAgtaagttgcgctattgcatcttgggtagttctagatctgaattgaagtatgtttc----tagaacctgcgtaaagactcttgtacgcttccgtgaccttggtacMapped 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|6022364|gb|AW067292.1|AW067292EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGANCGACAAGGACATCCAGGCAN
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|16927586|gb|BM080655.1|BM080655EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|78120826|gb|DV539210.1|DV539210EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|32867796|gb|CF007478.1|CF007478EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGAACGATAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|60394528|gb|DN227398.1|DN227398EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTACTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|76015306|gb|DT942476.1|DT942476EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST:
gi|32944133|gb|CF048952.1|CF048952EST: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC GTGTCCACGTGACATTGGAGTCCCTGCTGAACGATAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
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:
130GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
229GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
91GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
259GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttccatcattgtccacctctttatgaaataagacgttttcaataataaaactattttaatgttactcttcaaatgtcgccttctttttag
- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT