Sequence
atgc intronic sequence ATGC exonic sequenceTATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatcctttttgcttctattctttttatgttttgcgaaagggcctctaactgagttggttaggtggtttgagtagcactcctcaggtcctgggttcgac...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 13
TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatcctttttgcttctattctttttatgttttgcgaaagggcctctaactgagttggttaggtggtttgagtagcactcctcaggtcctgggttcgac-
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AATTATACTTAGAGGCGCAAATGACTTCATGCTAGATGAGATTGACAGATCATTGCATGATGCATTGTGCATTGTGAAGAGAACTCTGGAATCCAATATGgtataaccttttgcttctgttcctta-acatgttggttccctgcagttgaatatataaagttcactgttatattaagatttttgggagagtaagaaaaaaa
upper sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G12970.1 (Glycine max), 5'ss of exon 13
TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttttt----gcttctattctttttatgttttgcgaaagg----gcctctaactgagttggttaggtgg------tttgagtagcactcctcaggtcctgggttcgac---------------
| | || || ||||| ||||||||| |||||||||||||| ||| || | |||||||||| ||| ||||| |||||||| || |||||||||| |||| | | |||| || || || ||| || || | | | |||| | | || ||| | | |||| | | || |
TTTGATTCTAAGAGGTGCAAATGACCATATGCTTGATGAGATGGACAGAGCTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgcatacatagctttcatcctactttggttgaaatcaaaattttgctttagattaagtttttcaaatgaagtctttttatttttccttccttgtgctttattttttatatatataaaattcag
upper sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA05G29870.1 (Glycine max), 5'ss of exon 13
TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttttt----gcttctattctttttatgttttg--cgaaagg--gcctctaactgagttggttaggtggtttgagtagcactcctcaggtcctgggttcgac---------------------
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TTTGATTCTAAGAGGTGCAAATGACCATATGCTTGATGAGATGGATAGAGCTCTGCATGATGCATTGTCCATTGTCAAGAGAACTCTTGAATCAAATACGgtatcctgcatacgtagctttcatcctactttggttgaaatcaaaatgttgctttagattaagtttttcaaatgatgtctttt-tattttgccttccctgtgcttgattttttaatatataaaattcagMapped 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|9732094|gb|BE510846.1|BE510846EST: CATTGCATGATGCCCTGTGTATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTATCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
EST:
gi|89756397|gb|DY686447.1|DY686447EST: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
EST:
gi|32846877|gb|CD986558.1|CD986558EST: CATTGCATGATGCCCTGTGTATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
EST:
gi|44681818|gb|CK786866.1|CK786866EST: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
EST:
gi|211469891|gb|FL096480.1|FL096480EST: CATTGCATGATGCCCTGTGTATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
EST:
gi|211469889|gb|FL096478.1|FL096478EST: CATTGCATGATGCCCTGTGTATTGTGAAGAGAACCCTGGAATCAAATATG GTTGTTGCTGGTGGTGGTGCAGTTGANGCTGCGTTATCAGTTTACCTTGAG
genomic: CATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAG
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),
49 (downstream exon)
Score:
351TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAGAACCTTGCAACGACCTTGGGTTCTCGGGAACAATTGGCAATTGCTGAAT
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
146TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAGAACCTTGCAACGACCTTGGGTTCTCGGGAACAATTGGCAATTGCTGAAT
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
124TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAGAACCTTGCAACGACCTTGGGTTCTCGGGAACAATTGGCAATTGCTGAAT
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
109TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatccttt ... ggcaatatagGTTGTTGCTGGTGGTGGTGCAGTTGAGGCTGCGTTATCAGTTTACCTTGAGAACCTTGCAACGACCTTGGGTTCTCGGGAACAATTGGCAATTGCTGAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATAATACTTAGAGGCGCAAATGACTTCATGCTTGATGAGATTGACCGATCATTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAAATATGgtaatcctttttgcttctattctttttatgttttgcgaaagggcctctaactgagttggttaggtggtttgagtagcactcctcaggtcctgggttcgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA