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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCGTCCCTGGCTCAATTTATTCTGTAAGAGTGGTTGCAAAAGATGATCACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtgcctttttacaattatctgtgtcagtaaaaacgtttttgaatgactacctgtattccaaaatcatgtatgctcatcaacaatttgcataaacag

Basic information

species Oryza sativa
transcript LOC_Os01g19470.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19470.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GRMZM2G014788_T01 (Zea mays), 5'ss of exon 24
ACTCGTCCCTGGCTCAATTTATTCTGTAAGAGTGGTTGCAAAAGATGATCACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaag--------------tggtgcctttttacaattatctgtgtcagtaaaaacgtttttgaatgactacctgtattccaaaatcat----------gtatgctcatcaacaatttgcataaacag
||| || ||||| || | ||| ||| ||||||||| |||||||||| |||    |||||||||||||||||||||||||||||||||| ||||| || |||||||              ||  | |  |     ||| |   || ||| | |     |||| | | |  |  | |     |  | | |           |||||| | ||||| |||||||    ||
ACTTGTGCCTGGATCGACTTACTCTATAAGAGTGGCTGCAAAAGATAATCTTCAGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATTTGTCAGTTAATgtaagactaacataagcattgaagtccatcgcacattctgcttg-cagcatatcatattttcagttatgatttatgaatgaggaactttttattgtttatatgcttaacaaca-tttgcatttctag
















Mapped 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|163925522|gb|EG711587.1|EG711587
EST:     ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGAT                         GTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCG
genomic: ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCG
EST: gi|29684738|gb|CB681013.1|CB681013
EST:     ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGAT                         GTTGGTCAGGATGACATCTCTGGTA
genomic: ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTA
EST: gi|27547001|gb|CA765154.2|CA765154
EST:     ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGAT                         GTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCG
genomic: ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCG
EST: gi|58657305|gb|CK045985.1|CK045985
EST:     ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGAT                         GTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACC
genomic: ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACC
EST: gi|38482233|gb|CF966283.1|CF966283
EST:     ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGAT                         GTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCG
genomic: ACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACC-

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), 70 (downstream exon)
Score: 7

ACTCGTCCCTGGCTCAATTTATTCTGTAAGAGTGGTTGCAAAAGATGATCACAGGTTTGCAGCAGTTGAGCGTGCTTCACCTGAATATGTGTCAATTGATgtaagtggtg ... gcataaacagGTTGGTCAGGATGACATCTCTGGTATTGATTTTGTTGTTTTTGAAAGACCGGAATCAACAATTTTGAGTGGCCATGTGGAAGGAGATGATCTTGACATGT




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