Sequence
atgc intronic sequence ATGC exonic sequenceGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgct---ttctcttttgaaatattcttatcaaaggcttgtttttctttcctt
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GTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTGgtatgttgatttccac-ccttaagagtaatt--tctcagtggtttgatgtatgctgaaattattctagtggtaggctagtcataatgttgacagcataagtgg
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G06760.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattct-tatcaa-aggcttgtttttctttcctt
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GTGGATCCTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTAgtatgttgacctccttattttgctttgatgtacttaatttt--ttgtccaacttttccagcaccattatcttttgtatggacaaagtaataactcaaaatgt
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G36570.1 (Glycine max), 5'ss of exon 5
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
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GTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatgttggtattcttcctgtgcat-ttcactactttatacatgtatgctaccatgttaacagtggacgtggaatattaatatcatatgctacctaccccg
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G33950.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
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GTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatgtttgtattcttccagtgcat-ttcactactttatacatgtatgctaccatgttaacagtggacgtggactattaatgtcatatgctacctacccca
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacat-ccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
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GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGGAGTGCAAAAGTGCTGgtatgttgattt-cattctcagtacacacacacacacacacttttttttgtgtgcatcatcatatgtg-tgtgtctgtgtgtttcaacattttatcttgtca
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 5
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttcc--ttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
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GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGAAGTGCAAAAGTGCTGgtatgttgatttcattctcagtacacacactttttttgtgtgca-tcatcatatgtgtgcgtgtgtgtg-tttcaacattttat-cttgttacattgtaattt
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G43620.1 (Glycine max), 5'ss of exon 4
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttcc--ttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
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GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGAAGTGCAAAAGTGCTGgtatgttgatttcattctcagtacaaacactttttttgtgtgca-tcatcatatgtgtgcgtgtgtgtg-tttcaacattttat-cttgttacattgtaattt
upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt------
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GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtg---ttgaagaccatgtgtgctccttcttctttt---ttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctcMapped 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|33095534|gb|CF055528.1|CF055528EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST:
gi|18660957|gb|BM501137.1|BM501137EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST:
gi|6695759|gb|AW288837.1|AW288837EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST:
gi|13198123|gb|BG354164.1|BG354164EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG ATTCCTGGTGAACCGAACAT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACAT
EST:
gi|6587591|gb|AW244909.1|AW244909EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGNTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST:
gi|9825069|gb|BE575271.1|BE575271EST: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
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),
47 (downstream exon)
Score:
424GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
154GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
160GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
Block sizes:
48 (upstream exon),
46 (downstream exon)
Score:
157GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt
- - - - - - - - - - - CAAGCT