Sequence
atgc intronic sequence ATGC exonic sequencegtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 19
gtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
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gtaatattcatgatcttatattggttat-tacgtactaattatttaccatgtatattctaagccg-ttgatttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g04990.4 (Oryza sativa), 3'ss of exon 18
gtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG--------------
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gtaatattcatgtccttatactggttata--actaccaataatttgccatatatgttctaag-ctgttgattcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGGTAAATATGCTGAC
upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 18
gtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
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gtaatattcatgtccttatactggttata--actaccaataatttgccatatatgttctaag-ctgttgattcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGMapped 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|6194573|gb|AW146677.1|AW146677EST: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST:
gi|67023162|gb|CO451911.1|CO451911EST: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATTTATG GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAAAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST:
gi|93281969|gb|EB674233.1|EB674233EST: TGAAAATGTTTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST:
gi|6194494|gb|AW146598.1|AW146598EST: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
EST:
gi|50335868|gb|CO530994.1|CO530994EST: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATG GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
genomic: TGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGG
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:
45AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
154AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
128AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
44AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatattta ... tcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
ttctaaa putative branch site (score: 44)
tctcttgtttc CT-rich tract
ttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatttatgattctgtgttggctatatgaccatcagttatggccaagcatgttctaaatctcttgtttcggttgcagGCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG