Sequence
atgc intronic sequence ATGC exonic sequencegtaggccactgattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 9
gtaggccactgat--tggtagcactgcgttagagctcttcaatgattaa--ctttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
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gtaagttagaagttttggtgatattctgttattacgctg-gataatttattcttctttctggtccatagGTAGGTATCTTTGATGCCACAAACAGCACAAGAAACCGGAGAAATATGCTGATGAAAATGGCGGAAGGCAAGTGTAAG
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 12
gtaggccact------gattggtagcactgcgttaga--gctcttcaatgat--------taactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
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gtaaatcattcttgttgaatacttttgttactttaatatgttctttcatgttattttgcataagttttaatttcgatttagGTTGGGATATTTGATGCCACAAACAGTAGCAAGGAACGAAGAAACATGCTGATGAAATTGGCTGAAGGAAGATGCAAG
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaggccactgattggtagcac-tgcgttagagctcttcaatgattaactttcagctggt------ctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
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gtaagtatctttcggtttagatgtaagttcctggtttctatatcttgcattgtaaatagtttttagctgtagGTTGGAATCTTTGATGCAACTAATAGCACACGAGTTCGACGGAATATGTTGATGAAAATGGCTGAAGGAAAGTGTAAG
upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 10
----------gtaggccactgattggtagcactgcgttagagctcttcaat---gattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
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gtaagttattttatgtcagatattgtgatgcatgtgcctaatcctttcattttaaatta--ttctaattggattgtagGTTGGAATATTCGATGCCACAAACAGTACCAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGMapped 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|84980594|gb|DW530943.1|DW530943EST: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
EST:
gi|19437252|gb|BM953662.1|BM953662EST: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
EST:
gi|22491067|gb|BU050990.1|BU050990EST: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG GTTGGTATTTTCGATGCCACAAACAGCACAAGAATGCGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
EST:
gi|148957598|gb|EC903699.2|EC903699EST: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAG GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
genomic: CTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTG
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),
49 (downstream exon)
Score:
111GTGGCTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
128GTGGCTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
91GTGGCTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
427GTGGCTGCATTAGCAATGGAAGATATGCTATCTTGGATGCAGGAGGGTGGTCAGgtaggccact ... tggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
gattaac putative branch site (score: 427)
aatgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggccactgattggtagcactgcgttagagctcttcaatgattaactttcagctggtctgcagGTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA