Sequence
atgc intronic sequence ATGC exonic sequencegtatgaaaaaaactattagatgcattctagaaaaatatgccttatacttactattattttttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g51790.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
gtatgaaaaa--aacta---ttagatgcattctagaaaaatatgccttatacttactattatttt-ttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
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gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcaccttcttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
upper sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 26
gtatgaaaaaaa---------ctattagatgcattctagaaaaatatgccttatacttactattattttttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
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gtattacaaagaatttgtttcttattacatttgttctatgttttcctcccttaa--tgaaccttggggtttgat--tttctagGAACGCTCAGTTTCAACTATTGTTTATCTTGTTTCCCTTCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG
upper sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 25
gtatgaaaa--aaactattagatgcattctagaaaaat-atgccttatacttactattatttt----ttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
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gtaccatgatgaaccaactttttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG
upper sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S274_85V6.1 (Physcomitrella patens), 3'ss of exon 26
gtatgaaaaaaactattagatgcattctaga-----aaaatatgcct-------tatacttactattattttttgctc-------------ctttat-agGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
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gtatgatgtaaaacaccgattgtattttgaatgctcaaattgtgtgtaactgattgtgcatatccgagtgttatgctgagaagtcggtttgttttatcagGAACGCTCAGTATCGACAATACTGTACCTCGTCTCCCTTCAAGATCTGACACACTGCCCCTTTCGTGTGGTGGATGAGATCAATCAGGMapped 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|87019115|gb|CI297316.1|CI297316EST: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGG GAGCGATCAGTTTCAACCATCCT
genomic: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGGgtatgaaaaa ... tcctttatagGAGCGATCAGTTTCAACCATCCT
EST:
gi|66914986|gb|CX101834.1|CX101834EST: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGG GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
genomic: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGGgtatgaaaaa ... tcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
EST:
gi|218486434|gb|FG966621.1|FG966621EST: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGG GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
genomic: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGGgtatgaaaaa ... tcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
EST:
gi|29628420|gb|CB633431.1|CB633431EST: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGG GAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
genomic: GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGGgtatgaaaaa ... tcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACC
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:
64 (upstream exon),
63 (downstream exon)
Score:
14GCAAACAGGTCAGTTGCAGGTGTTGAGCGCTCATCACCAATCTGGAGGGgtatgaaaaa ... tcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcattctagaaaaatatgccttatacttactattattttttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG
tacttac putative branch site (score: 14)
ttattttttgctcctt putative PPT
ttatacttactattat TA-rich tract