Sequence
atgc intronic sequence ATGC exonic sequencegtgacttccattttgcacagctatcctgacatcattgcaacccctagtttggttatgatggatctacacaatcttgaacttaccaaggttctttttctttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g09360.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G350818_T01 (Zea mays), 3'ss of exon 12
gtgactt--ccattttgcacagctatcctgacatcattgcaacccctagtttggttatgat-ggatctacacaatcttgaacttaccaaggttctttttctttc--ctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
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gtgactttaccatttt-cacagctatagtaacatagctgca-------gtgtgcacataacaggattttctgcgttttgaagtcaccatggttcttttgctttcaactgcagGACCTTGTCGGCTTAGTCATCTCAATACTGCTTCTTGCAGATTTCAGCTTAGTCTTGCTTACTTTCCTCCAACTATATTCATATTCTATGGTCGATGTTC
upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA06G09360.1 (Glycine max), 3'ss of exon 19
-------gtg-acttccattttgcacagctatcctga-catcattgcaacccctagtttggttatgatggatctacacaatcttgaacttaccaaggttctttttctttc--ctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT------------------------------------------------------------------------
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gtatctcttgtattgatagtttgtactgatgtggtaaacaaaattgccaattcttgtgcttgcatcatttgataactaatttctttatttttccttttcctttatgtgttgactgcaggatcttgttggtttagtaatctcaatgctgcttctaggagattttagtttagtattacttaccttgcttcagTTGTATTCAATTTCTTTGGTGGATGTCTTCCTTGTGTTGTTTATATTACCTTTCGGCATTCTTCTCCCATTTCCTGTCGGAATTAATGCTCTCTTTAGTC
upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 20
gtgacttccattttgcacagctatcctgacatcattgcaacccctagtttggttatgatggatctacacaatcttgaacttaccaaggttctttttctttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
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gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactg-atttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCTMapped 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|66924763|gb|CX111611.1|CX111611EST: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAG GATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
genomic: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAGgtgacttcca ... tttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
EST:
gi|9457279|gb|C72119.2|C72119EST: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAG GATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
genomic: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAGgtgacttcca ... tttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
EST:
gi|29616295|gb|CB621307.1|CB621307EST: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAN GATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGC
genomic: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAGgtgacttcca ... tttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGC
EST:
gi|33802261|gb|CF327003.1|CF327003EST: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAG GATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
genomic: TTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAGgtgacttcca ... tttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTA
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:
50 (upstream exon),
69 (downstream exon)
Score:
11AGTTCTCGACATTGACAACTTAAGGACACTCAAGGACAAGAGAGATTTATTTTACCCTCTTTCTCTTATATTGCACAATACCAAACCAGTTGGGCATCAGgtgacttcca ... tttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgatggatctacacaatcttgaacttaccaaggttctttttctttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
aacttac putative branch site (score: 11)
ttctttttctttcctg putative PPT
tttttcttt TA-rich tract