Sequence
atgc intronic sequence ATGC exonic sequenceACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaacatttatttcgaggcatactttggtcacttgactatttgggtgaaaaggcttatatgtatggatgggtgtttgataaatgataacttccct...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 13
ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaacatttatttcga-ggcatactttggtcacttgactatttgggtgaaaaggcttatatgtatggatgggtgtttgata-aatgataacttccct--
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ACAATTATTTCTGGGATGGGTGAGCTGCATTTGGATATCTATGTTGAACGCATCAGGAGAGAGTACAAGgtaatgta-tacttaggtcaatggcatgattcgttcccctggctatatgtgcaatgcaattta---ggattgatggatgtttattgtactaaaagcttgtctgt
upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 5'ss of exon 13
ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaacatttatttcgaggcatactttggtcacttgactatttgggtgaaaaggcttatatgtatggatgggtgtttgataaatgataacttccct--------------------------------------------------
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ACAATTATTTCTGGAATGGGAGAGCTGCATTTGGACATTTACGTTGAACGCATTCGGAGGGAGTATAAGgtgcctggtc-tttttgtctttctttaatacagtgatggga---ttctagtatgattgctaattcg-attctagtatgattgctaattcaaaatcttcacctgtatacttaagtactctctctttccctctttaatttacctttatgaag
upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 13
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 5'ss of exon 11
ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaa-acatttatt-tcgaggcatact-ttggtcac-ttgactatttgg--gtgaaaaggcttatatgtatggatgggtgtttgataaatgataacttccct--------------------------------------------------------------------
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ACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAGgttcttaatacattgattctttatactttttaccaaccacgttaggtattttgtcatgagttgacacat-tatctcaaggtcctctcaagtgtcctctaccgatcttttaaggtatagtcaggagatggacaccgtatactcactgctgttaatgcttggctatttttctgcag
upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ36205 (Selaginella moellendorffii), 5'ss of exon 13
ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaacatttatttcgaggcatactttggtcacttgactatttgggtgaaaaggcttatatgtatggatgggtgtttgataaatgataacttccct
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ACCCTCATTTCGGGGATGGGGGAGCTGCATCTTGACATTTACGTGGAACGCATGAAGAGAGAATATAAGgt--tgacaggtgcacttc------tgttttgctcttcatgacgctgaagctatcag-------------------------------------------Mapped 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|91874831|gb|EB404788.1|EB404788EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|6194594|gb|AW146698.1|AW146698EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|6020648|gb|AW065681.1|AW065681EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|211410070|gb|FL355701.1|FL355701EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|211409847|gb|FL347405.1|FL347405EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|67017174|gb|CO445923.1|CO445923EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST:
gi|211430479|gb|FL350077.1|FL350077EST: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG GTGGATGCAAAGGTWGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
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:
39 (upstream exon),
49 (downstream exon)
Score:
167ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
Block sizes:
39 (upstream exon),
48 (downstream exon)
Score:
175ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
Block sizes:
39 (upstream exon),
49 (downstream exon)
Score:
199ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
Block sizes:
39 (upstream exon),
49 (downstream exon)
Score:
121ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaacatttatttcgaggcatactttggtcacttgactatttgggtgaaaaggcttatatgtatggatgggtgtttgataaatgataacttccct
- - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA