Sequence
atgc intronic sequence ATGC exonic sequence...aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
-aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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gtattgattaacacagtgtaaagataggttttgaaatattgattagttcattttaatttttcttctgatttagcgttttattacttggatctacaa-tcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 19
-aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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tgatgaacacagatagtgtaaagataggttttgaaatattgattacttcattttaatttttcttctgatttagccttttattacttggatctacaa-tcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaacct---tttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
| | | || || | || | | | | | | | | ||| | ||| | | | | ||||| | | | ||| |||||||||| |||||||| | ||||| | ||||| |||||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||||||||||||||
gtaagtttagcactcttgattttaaaagaatcgcgaggttagatgg--tttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 19
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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ttaagcgatgtaagacacagaattctatactagcctgtttatccatggcctttttgcttccatttgatttttaccc--ctggccacatttttcattga-tcagATATGTAAAACGCGCGCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 4
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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ttaagcgatgtaaaacacagaattctatactatcctgtttatccatggcctttttgcttccatttgatttttaccc--ctggccacatttttcattga-tcagATATGTAAAACGCGCTCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------aatgaattgttcctgt--tctttgttaactgtctacttc---ctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaat-tagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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gtaagttctaatacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacggga-aggactgcc---gctcaatttttattttgttggaatgcagATATGTTAATAGAGCTCTCTACTTGCTACATTTAATATGCGGTCCTTCTCACCCAAATACTGCTGCGACATATATCAATGTAGCCATGATGGAAGAGGGTMapped 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|29625529|gb|CB630540.1|CB630540EST: TCTTGCTGTGTTCTACTTACCGTTTACAACATACAGAACTGGCTCTAAA GTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCA
genomic: TCTTGCTGTGTTCTAC-TACCGTTTACAACATACAGAACTGGCTCTAAAgtaagttgac ... tttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCA
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 1 RNA-Seqlibrary.
Block sizes:
47 (upstream exon),
67 (downstream exon)
Score:
7ATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCTACTACCGTTTACAACATACAGAACTGGCTCTAAAgtaagttgac ... tttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
gattaac putative branch site (score: 7)
ccttttctattttt CT-rich tract
attaaccttttctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - gttcctg
- - - - - - - - - - - - - - - - -cttcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctgt