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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctttgctccctgtcaatgtgatcaggaaaaaagttgaatacaattaacagcatttcctttgtgaaacttgcaactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGATAAAAAGGATTAATCGTGCCCTTGATTTGTATGATGAGTTCCGTATAGAC

Basic information

species Oryza sativa
transcript LOC_Os07g43390.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G100730_T01 (Zea mays), 3'ss of exon 2
-----------gtaatcctttgctccctgtcaatgtgatcagga---aaaaagttgaatacaattaacagcatttcctttgtgaaacttgcaactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGATAAAAAGGATTAATCGTGCCCTTGATTTGTATGATGAGTTCCGTATAGAC-
           |||    | |  |   |||| || | ||  | |      |   || |    |   ||||    ||   | |   |||| ||| | | |||||| |||||||||| |||| |||||||||||| ||| |||  |||||||||||| ||||||||  ||| |||||| || |||||||| | | |||| ||  
ctatggaacatgtatcaatatttttattgtccatattatttgtatttgttatcctgtaccacacctacagggcatctcct-tatcactttcaattctgcagTCCGTTGTACGACTAGAAATCTATGGAAGCAGATGGCTTTTCATGGTGGATAAAGAGGATTAAATGTGACCTTGACTTATATGATGAATAC-GTATTGATC

upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G013811_T01 (Zea mays), 3'ss of exon 8
---gtaatcctttgctccctgtcaatgtgatcaggaaaaaagttgaatacaattaacagcatttcctttgtgaaacttgcaactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGATAAAAAGGATTAATCGTGCCCTTGATTTGTATGATGAGTTCCGTATAGAC
     |||  |||  ||      | |  |   |   |  |   || |    |   ||||    ||   | |    ||| ||| ||| ||||||||||||||||||||||||||||||||||| | | |||  |||||||||||| |||||||| ||||||||||||||||||||||| |||||||| |||
gtatcaatatttttgtcgtccatattcggtgtatttattatcctgtaccacagccacagggcatctcat-tatcgcttacaattttgcagTCCATTGTACGACTGGAAAGCTATGGAAGCAGATTGTTTTTCATGGTGGATAAAGAGGATTAAACGTGCCCTTGATTTGTATGATGAATTCCGTATTGAC
















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|218503567|gb|FG951513.1|FG951513
EST:     AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG                         TCCATTGTACGACTGGAA-GCTATGGA-GCAG-TGGATTTGAATG
genomic: AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAGgtaatccttt ... aactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATG
EST: gi|218485155|gb|FG948396.1|FG948396
EST:     AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG                         TCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGAT
genomic: AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAGgtaatccttt ... aactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGAT
EST: gi|218501179|gb|FG958401.1|FG958401
EST:     AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG                         TCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGAT
genomic: AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAGgtaatccttt ... aactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGAT
EST: gi|27577080|gb|CA999774.1|CA999774
EST:     AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG                         TCCATTGTACGACTGGAAAGCTAT
genomic: AGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAGgtaatccttt ... aactttacagTCCATTGTACGACTGGAAAGCTAT

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: 40 (upstream exon), 69 (downstream exon)
Score: 18

GACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAGgtaatccttt ... aactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGATAAAAAGGATTAATCGTGCCCTTGATTTGTATGATGAGTTCCGTATAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaagttgaatacaattaacagcatttcctttgtgaaacttgcaactttacagTCCATTGTACGACTGGAAAGCTATGGAAGCAGGTGGATTTGAATGGTGGATAAAAAGGATTAATCGTGCCCTTGATTTGTATGATGAGTTCCGTATAGAC
               aattaac  putative branch site (score: 18)
       ttgaatacaattaa  TA-rich tract