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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAACCGAGAGAGCTGGGGAAGATGTTCTTCCTTGGGGGCAGCGAGTGATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttctttcttttctcatttttgatgtccatctattgcatgaccatactgtccttttttcatagggtaacttaccttagatatttttgttaacac...

Basic information

species Oryza sativa
transcript LOC_Os06g40730.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40730.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G092895_T01 (Zea mays), 5'ss of exon 13
TTCAAACCGAGAGAGCTGGGGAAGATGTTCTTCCTTGGGGGCAGCGAGTGATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttctttcttttctcatttttgatgtccatctattgcatgaccatactgtccttttttcatagggtaa--cttaccttagatatttttgttaacac--
 |||||||||||||||||||||||||||||||||||||| | ||| ||||||||||  ||   |||||| |  ||||| || |||| |||||||| |||||||  | |||||   | | | | |   ||     |    ||| ||| | | |      | | || ||  | ||   | ||  ||  | | | | ||| ||    
CTCAAACCGAGAGAGCTGGGGAAGATGTTCTTCCTTGGGTGGAGCTAGTGATGGATTGTCATCAGGCGAACAGCCTGAGATACCTAATCATAAGCTTAAGgtacat-ttcttcagtgtgttacta--gacccttaagatttgaatg-ctagaaatctttgtgtttatttgctactccctatgttcaaaactatagttcacttta
















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|58595357|gb|CF993665.1|CF993665
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATGCGGGTAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
EST: gi|88671997|gb|CI726113.1|CI726113
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCCTTGGCAACACCACTGAGAAGGAT
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCC-TTGGCAACACCACTGAGACGGAT
EST: gi|89172448|gb|CI721507.1|CI721507
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTNA-GGGCCTTGGCAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCT-ACGGGCCTTGGCAA
EST: gi|88671150|gb|CI725266.1|CI725266
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACNGCTA-GGGCCTTGGCAACACC
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGAC-GCTACGGGCCTTGGCAACACC
EST: gi|88674443|gb|CI728556.1|CI728556
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCATTGAGAAGGATA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATA
EST: gi|88672670|gb|CI726786.1|CI726786
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAGAAGGATACGAAGGAAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
EST: gi|88673380|gb|CI727493.1|CI727493
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTG
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTG
EST: gi|29629190|gb|CB634201.1|CB634201
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
EST: gi|88667182|gb|CI719318.1|CI719318
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
EST: gi|88677007|gb|CI731120.1|CI731120
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGG
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGG
EST: gi|29616357|gb|CB621369.1|CB621369
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAA
EST: gi|88908563|gb|CI713121.1|CI713121
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCT
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCT
EST: gi|88673085|gb|CI727200.1|CI727200
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCACTGAG
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAG
EST: gi|88593829|gb|CI713783.1|CI713783
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACACCAC
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCAC
EST: gi|88673190|gb|CI727304.1|CI727304
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAA
EST: gi|88669516|gb|CI723434.1|CI723434
EST:     ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAG                         AGCATGACGCTACGGGCCTTGGCAACA
genomic: ATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACA

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: 72 (upstream exon), 46 (downstream exon)
Score: 14

TTCAAACCGAGAGAGCTGGGGAAGATGTTCTTCCTTGGGGGCAGCGAGTGATGGATCATCCCTAGGCGAGCGCCCTGAAATTCCTAGTCATAAGCATAAGgtatgtcttc ... ggaactgtagAGCATGACGCTACGGGCCTTGGCAACACCACTGAGACGGATACGAAGGAAACCGCTCGCTATACCAAAGGAGAGGAAGAATCGATCTCTATGGAAGAGGC




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