Sequence
atgc intronic sequence ATGC exonic sequenceGTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178996_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g55150.2 (Oryza sativa), 5'ss of exon 6
GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtg--attccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata
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GGTCGGCTGTTGGATTTAGATTGGATAGCCTTCTTAAACTCATTGATATTCGGGCACGTAATAATAGGATGACTCTCATGCATTATTTATGCAAGgtatggcatttaatttcagtaatcccatcgttttttgtgttttgaagtgtcactgaaccacatagttatgaaagcattgc--tcgttttgcgggaatttact
upper sequence: GRMZM2G178996_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G36440.1 (Glycine max), 5'ss of exon 17
GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgt----gtgattccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata
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GTTCTGCTATTGGATTCAGATTGGATAGCCTTCTTAAACTCACAGAGACACGTGCCCGGGATAAGAAGATGACTCTCATGCATTATCTTTGTAAGgtacatgttgctatttattcctttttgtttttttttaaatctttcaaaattatatttcgaattattaatttc-tattttcggtttttctttcttttctttt---
upper sequence: GRMZM2G178996_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G33930.1 (Glycine max), 5'ss of exon 12
GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata------
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GTTCGGCTGTGGGGTTTCGATTGGATAGTCTCCTTAAACTCACTGATACACGAGCCAGAAACAACAAGATGACTCTTATGCATTATCTTTGTAAGgtaaa----cgacctggtctcc-ttaaat-ttcaatattaattgtttctgtacaaggagtttagttcctcctttgtgtacaaattgtaagtaaaatgatactgttt
upper sequence: GRMZM2G178996_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0008g06530.t01 (Vitis vinifera), 5'ss of exon 15
GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata--
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GTTCTGCTATTGGATTTCGATTGGATAGTCTCCTTAAACTCACTGATACACGAGCCCGGAACAACAAGATGACTCTCATGAATTATCTTTGTAAGgtac-attatttttcacttgggttgatgctttatatttcctatcaattttgtcaatcaaaccaacctaagttggttctcaac-tattaacacagccaattggMapped 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|211470382|gb|FL227254.1|FL227254EST: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|211470380|gb|FL227252.1|FL227252EST: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|211467359|gb|FL096460.1|FL096460EST: AGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
genomic: AGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|211470381|gb|FL227253.1|FL227253EST: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|211470378|gb|FL227250.1|FL227250EST: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTCCA
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|211470379|gb|FL227251.1|FL227251EST: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCA
EST:
gi|32800407|gb|CD952643.1|CD952643EST: ATATACGAGCACGTAATAATAGGATGACTCTGATGCATTATCTATGCAAG GTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATC
genomic: ATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATC
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:
47 (upstream exon),
48 (downstream exon)
Score:
32GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCAAATTTAGAACCTGCCTCAAAG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
28GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCAAATTTAGAACCTGCCTCAAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
70GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCAAATTTAGAACCTGCCTCAAAG
Block sizes:
46 (upstream exon),
47 (downstream exon)
Score:
13GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattcc ... gtttgtacagGTTCTTTCGGACAAGCTTCCTGAAGTGCTTGACTTCAGCAGGGATCTTGCAAATTTAGAACCTGCCTCAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGCAGCTGTTGGATTTAGATTGGATAGTCTTCTTAAGCTCAGTGATATACGAGCACGTAATAATAGGATGACTCTCATGCATTATCTATGCAAGgtgtgattccctcctcctctcccttagacattcagtctaacaaggttatgtctaagcatatcgatggcacagtgtcatcattgttatgacataggtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcctcc