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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggattaatttttactcccaatattatcgcggactagcaatttcttgtgatttcttgagttgctttcttactgccaaattatcaatttataatcc...

Basic information

species Oryza sativa
transcript LOC_Os07g30980.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g30980.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G121427_T01 (Zea mays), 5'ss of exon 10
ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggattaatttttactcccaatattatcgcggactagcaatttcttgtgatttcttgagttgctttcttactgccaaattatcaattta--taatcc
|| ||||||||||| ||||| |  || ||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||  ||||||| | ||||  ||| |   |  |  | |  ||| | |   |    |     |       | ||  |      | || |   |||   |     
ATAACTGGCAAAGCTTTCCAAGTCTCCTTCCGCAACAGGAAAATTCCCTTTAACATTCATGGTGTGGCTTTCTACAGGAAAAAGgtagttggatttagttttcttccaagattcgttacag--taggagtgcatgaaaaacaactattcatgtgtccgaaccttgacttgttggttttgttgggtt

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA20G34060.1 (Glycine max), 5'ss of exon 12
ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggattaatttttactcccaatattatcgcggactagcaattt--cttgtgatttcttga-gttgctttcttactg--ccaaattatcaatttataatcc-
||  | || ||||| |||||   | | |||||  | || ||||| || ||||| ||||||||||||||||| ||||| ||||||||  ||       ||||  |   ||| || |    | | |   |  ||   || | |||   ||  |||    | ||| |   || |   ||  | | ||||    
ATATCAGGTAAAGCCTTCCAAATGGCTTTCCGTGATAGGAAAATACCATTTAACATTCATGGTGTGGCTTTTTACAGAAAAAAGgtaattt------ttttgccaatcaagataaagatgtatttatatcttactttctaattgactgttgttaaaatattaatattcctaggcatgcactaataactta

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT4G25120.1 (Arabidopsis thaliana), 5'ss of exon 12
ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgt-----gcttggattaatttttactcccaatattatcgcggactagcaatttcttgtgatttcttga-gttgctttctta-ctgccaaattatcaatttataatcc-----------------------------------------------------------
 |  | || ||||  || ||     |||||||| | |||||||| || |||||  |||||||||| ||||||||||||||||||||     || |     |  | | | |    | | | | ||    |  | |  | |    || | ||||  |||     | | | ||    ||||       | ||                                                             
GTGTCAGGTAAAGTGTTTCAAAATGCATTCCGCCAGAGAAAAATACCATTTAACGTTCATGGTGTTGCTTTCTACAGGAAAAAGgtagattgcctcagaaatatctcatttgttaaactgttgcatgatcactaagtatctcaatgttttgacattgacaattcatccgcatggttattgtagctttatttgtttcggacaataagctccatctactaaacataacagctatcaactttttccacgttag

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv16s0013g00300.t01 (Vitis vinifera), 5'ss of exon 11
ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggattaatttttactcccaatattatcgcggacta-gcaatttct-tgtgatttcttgagttgctttcttactgccaaattatcaatttataatcc-
 |  |||| |||| ||||||  |  | || ||  | || || || || ||||| |||||||||||||| |||||||||||||||||  |     |  |  |    |    ||  |    |   || || || | | ||  |||| |  | |    || | | | ||  || ||    | || |||  
GTATCTGGAAAAGTATTCCAAACAGCCTTTCGTGATAGGAAGATACCGTTTAACATTCATGGTGTGGCCTTCTACAGGAAAAAGgttatcaacatcctcatcctccaatttacaaaaatgttgtatgcgatatttatgcaatttttatattgaaattttgattccc--atcatttgct-atgatcat

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|88509079|gb|CI436585.1|CI436585
EST:     ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTGTACAGGAAAAAG                         GTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
genomic: ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggat ... actatttcagGTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
EST: gi|58662033|gb|CK050713.1|CK050713
EST:     ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG                         GTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
genomic: ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggat ... actatttcagGTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
EST: gi|88592693|gb|CI710815.1|CI710815
EST:     ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG                         GTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
genomic: ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggat ... actatttcagGTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
EST: gi|88371820|gb|CI680930.1|CI680930
EST:     ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG                         GTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT
genomic: ACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggat ... actatttcagGTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGAT

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: 37 (upstream exon), 42 (downstream exon)
Score: 3

ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAGgtgcttggat ... actatttcagGTTATCAAAGCAATTATGGCCATACTTAAAACTACATTACCAGGCTGTGATGATGATGCCCCATGGCATCAAGCCTTCAAGGCCATTCTTCCTGGTGACA




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