Sequence
atgc intronic sequence ATGC exonic sequenceGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctggaaacatttatgtataagaggcattccgatgttgttactgaatagttatgactggaatcactaaacaaaaatgcaccc...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 12
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct-----tat----gcaaatctggaaacatttatgtataagaggcattccgatgttgttactgaatagttatgactggaatcactaaacaaaaatgcaccc
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GATATTTGAGGAGGCTGGTTGTGATACACCAGCTAGCCCTAGTTGTGGTGCTTGTTTGGGTGGTCCTCGTGATACATATGCTCGCATGAATGAACCTATGgtaagtgcctccaaatatttcagtaaaacaggaaatgttgtttcgtatgaactttatcaacatagt-----agaatttatagatgtcttccttgaaagataaggt----
upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 14
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctggaaacatttatgtataagag-gcattccgatgttgttactgaatagttatgactggaatcactaaacaaaaatgcaccc-
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GATATTTGAAGAAGTTGGGTGTGACACACCAGCTAGTCCTAGTTGTGGTGCTTGTTTGGGTGGCCCAAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttctgccccaacatcttgtaatatactagtgtagttcaa--attctacttgttacttttatccttattatattgaaggaattgcaaata
upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatctta-tgcaaatctggaaacattta-tgtataagaggcattccgatgttgttactgaatagttatgactggaatcac-taaacaaaaatgcaccc
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GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttactt-ttatccttattattatattgaaggaattgcaa--
upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 14
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctggaaacatttatgtataagaggcattccgatgttgttactgaatagttatgactggaatcactaaacaaaaatgcaccc---
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GATATTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTACCTGTGGTGCTTGTATGGGTGGTCCTAGAGACACATATGCACGCATGAATGAACCTCAGgcaag-atattgttttcctcttggtacaactttaaaaagcatttcatcaactattccacct--atacttctgcttttattcctcagatgaaacccctaactta
upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 14
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctggaaacatttatgtataagaggcattccgatg-ttgttac-tgaatagttatgactggaatcactaaacaaaaat---gcaccc------
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----TTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTAGTTGTGGTGCTTGTTTGGGTGGCCCTAGAGACACATATGCACGCATGAACGAACCTCAGGCAAgt-tattattcatcttggtaaaccttt------aaaaggcattttatcaactattccatgcccacttttgcttttattcaccagaagaaaatcatatagcctgtttgMapped 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|24769037|gb|CA404166.1|CA404166EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|7162228|gb|AW519835.1|AW519835EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|91051661|gb|EB162079.1|EB162079EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTTTGCGTGTCCACCCCGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|7137997|gb|AW499377.1|AW499377EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|86473276|gb|DY239646.1|DY239646EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTTTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
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:
45 (upstream exon),
38 (downstream exon)
Score:
23GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
45 (upstream exon),
48 (downstream exon)
Score:
89GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
47 (upstream exon),
46 (downstream exon)
Score:
61GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
43 (upstream exon),
45 (downstream exon)
Score:
24GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctggaaacatttatgtataagaggcattccgatgttgttactgaatagttatgactggaatcactaaacaaaaatgcaccc
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