Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaattactctatgttctgagtatagtttcattactgcctaataaacaacaatttaatgctgctatttgaaccgttgattctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 8
gtatgttaattactctatgttctgagtatagtttcattactgcctaataaacaacaatttaatgctgctatttgaaccgttgattctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
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gtatgttgattactctaccttcagggttgtggttcattgataactgatagtttgtaattttctg-tgtgctttgaactgacaattttctttcagGCTTACATGTATGGGTTTTTCAAGAACAAGCGCATTGTTCTCTATGACACGTTGATTCAGCAG
upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 7
gtatgtta-attactctatgttctgagtatagtttcat-tactgcctaataaacaacaatttaatgctgctatttgaaccgttgat---tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG-
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ttatgttgtaaaaaataaagtatagaaaatagtctttcatgtcatatttttatcttcagtttgtaaatttgcttgaaataatttctatatatattgcaggCCTATATGTATGGATTCTTCAAGAACAAGAGGATTGTGCTTTATGACACATTAATTCAACAGG
upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 8
-gtatgttaattactctatgttctgagtatagtttcattactgcc-taataaacaacaattt--aatgctgct--atttgaaccgttgat-tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
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cttatgtct-taaaaaaaggtatagaaaatagtctttcatatgtcatttttatctccagtttgtaaagttgcttgaaataatttatctatatatattgcagGCCTATATGTATGGATTCTTCAAGAACAAGAGGATTGTCCTTTATGACACATTAATTCAACAG
upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttaattactc-tatgttctgagtatagtttcattact---gcctaataaacaacaatt-taatgctgctatttgaaccgt----tgattctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
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---caataatttcttgtggtttctcactatatgcttactgatttaatttgagatataatttttctcttgttgtgtgctaactcatattatgaaaaccatgcagGCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGMapped 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|32909801|gb|CF014613.1|CF014613EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTANNNNNNNNNCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
EST:
gi|76293281|gb|DV032849.1|DV032849EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTATG
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATG
EST:
gi|76293280|gb|DV032848.1|DV032848EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
EST:
gi|71761327|gb|DR959264.1|DR959264EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAACCCACAGTAAT GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
EST:
gi|7162447|gb|AW520069.1|AW520069EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
EST:
gi|6194775|gb|AW146879.1|AW146879EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
EST:
gi|71758092|gb|DR956029.1|DR956029EST: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAAT GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
genomic: TGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACA
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:
48 (upstream exon),
45 (downstream exon)
Score:
79AGTCCTCAGGGAAAAAATAGAGAAGCTGGCAGCTTCCCTCAAGTTTCCTTTGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
53AGTCCTCAGGGAAAAAATAGAGAAGCTGGCAGCTTCCCTCAAGTTTCCTTTGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
62AGTCCTCAGGGAAAAAATAGAGAAGCTGGCAGCTTCCCTCAAGTTTCCTTTGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
Block sizes:
47 (upstream exon),
47 (downstream exon)
Score:
61AGTCCTCAGGGAAAAAATAGAGAAGCTGGCAGCTTCCCTCAAGTTTCCTTTGAAAAAGCTTTTCGTGGTAGATGGGTCTACCAGATCAAGCCACAGTAATgtatgttaat ... tctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcctaataaacaacaatttaatgctgctatttgaaccgttgattctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
ttctctttc CT-rich tract
taataaacaacaattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaattactctatgttctgagtatagtttcattactgcctaataaacaacaatttaatgctgctatttgaaccgttgattctctttcagGCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC