Sequence
atgc intronic sequence ATGC exonic sequencegtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 5
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatc--taacttgca--------------tactgcattttaa----accaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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gtgagattcaagttttctttttttcatt-gacattctcaa----tttgtgttaaacgccaattgc-atctgttgtccactttttgtttcacaaatttggattca-aacattcgaatgaatagtttgcagggatcaaaacaattgtttcattttacttacagtgcagaaattgatag--tgtgatttgtgttattgcagGGCTCCAATATCTCAAGGATATGGCTTGACTGAAACCTGTGCTGGTGGGACATTTTCAGAGTATGATGAAACATCTGTTGGTCGCGTTGGTCCCCCTTTG
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 6
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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-----------------------------------------------------------tagaattgtctagctttatcatgtactttttctg-ttttgctttacagatttc---------ctgtattatcttttttctgtca----catttata---tttggttttcatttt--cagTGCTCCAATAGGTCAAGGATATGGTCTAACAGAGACTTGTGCTGGTGGGTCATTCTCTGATTTTGACGATACATCTGTTGGACGTGTTGGGCCACCTGTT
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 6
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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-----------------------------------------------------------aggaaatatttctagct--------tttactgtagt---gctttttcttttttgctttttgcgtttcctttattattcttgctg---tcatttataatttatgg-tcatatt----cagTGCTCCAATCGGTCAAGGATATGGTCTTACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTCGGCCGTGTTGGACCACCTCTT
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 6
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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-----------------------------------------------------------------------aaaggaaatattactggcttttactcaagtgctttttcttt---tttgatttttgcgtttcctttattatt----tattctgtgatttataatttatggtcatatagTGCTCCAATCGGTCAAGGATATGGTCTCACAGAGACTTGTGCTGGTGGGACATTCTCTGATGTTGATGATACATCTGTTGGCCGTGTTGGACCACCTCTT
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtccacttgtgtttactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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---------------------------------------------------------------------gtaaacgaatccctgaatatc-tccttgaggcttgctactctccaatatatctt------ttcgtccctttccatttctat-----gatctaacactgatattcctcagGGCTCCAATCGGTCAGGGATATGGGCTCACAGAGACTTGTGCTGGTGGAACCTTCTCGGAGTTTGAGGACACATCCGTTGGCCGTGTTGGTGCTCCACTT
upper sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 8
gtgagatagtactcttcattattttataagccattctcaagtctcttttgttaatatcaagttattgtttttggtc-cacttgtgtt-tactgtgattgaacttcacaatattcaaatctaacttgcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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------------------------------------------------------------------atttaaggaaacacttagctggcaatgtcctacaatcatgcagtatgcaatattatccttcctcttg---ttgtaattgctctaagtgaactgtcat-----------tttcagTGCTCCAATAGTTCAAGGGTATGGCCTGACAGAGAGTTGTGCTGGTGGTACATTTTCCGAGTATGATGATACATCTGTTGGTCGTGTTGGTGCTCCACTTMapped 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|58671144|gb|CK059830.1|CK059830EST: GGAGCACCTCTGTCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG GGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCCGGCGGGAC
genomic: GGAGCACCTCTGTCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtgagatagt ... gctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGAC
EST:
gi|86904934|gb|CI310727.1|CI310727EST: GGAGCACCTCTGTCTGGAGATACTCAGAGATTTATCAATATATGCCTTGG GGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGAC
genomic: GGAGCACCTCTGTCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtgagatagt ... gctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGAC
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:
41 (upstream exon),
72 (downstream exon)
Score:
6AGAAGGTGCGTGCGATCTTGGGAGGAAGGATTCGATTTATACTTTCAGGTGGAGCACCTCTGTCTGGAGATACTCAGAGATTTATCAATATATGCCTTGGgtgagatagt ... gctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatactgcattttaaaccaaaacaattgacaggttttgggttgtgctgttgcagGGCTCCAATAGGGCAAGGATATGGTCTTACTGAAACATGTGCTGGCGGGACATTTTCCGAGTATGATGACAATTCTGTTGGCCGTGTTGGTGCTCCATTG
aattgac putative branch site (score: 6)
attttaaaccaaaa TA-rich tract