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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgcgctatatctcacccctccagttgtcgtcgatgaaattaacagcaagtatgctggcataatggaattcatcttaaccttttcttaatcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACGAGGACATCATGAGGCTGACAGAGAATTTGAGCGAGAAATACATCATTGG

Basic information

species Oryza sativa
transcript LOC_Os06g03970.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 22
gtatgtgtgcgctatatctcacccctccagttgtcgtcgatgaaattaacagcaagtatgctggcataatggaattcatcttaaccttttcttaatcatatt-cagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACGAGGACATCATGAGGCTGACAGAGAATTTGAGCGAGAAATACATCATTGG
                  |      |    ||||  | |   | || ||  |||  |    || |  |   | | ||||||    |||| ||| | || ||| |||| || |||||||| || ||||| ||||||||||||||  | || || ||||||||||||||||||||||| |||||  |||||||||| |||||||| ||
----------------gtttgtttgtttgtttgt--ttgtgcatatgaattgcac-tgcagtgtcccaggaggactcatctatcactttccttgaccacattgcagGGCCACCAAAGCTGGTGGTTCTTCAGATGGACATGGCCGTGCACACGTACGAGGACATCATGAGGCTGACCGAGAACCTGAGCGAGAAGTACATCATCGG
















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|58602629|gb|CK013157.1|CK013157
EST:     AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAG                         GACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
genomic: AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
EST: gi|58662405|gb|CK051091.1|CK051091
EST:     AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAG                         GACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
genomic: AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
EST: gi|58660475|gb|CK049155.1|CK049155
EST:     AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAG                         GACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
genomic: AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
EST: gi|58676259|gb|CK064946.1|CK064946
EST:     GCCAGTGCAAG                         GACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
genomic: GCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
EST: gi|58597993|gb|CK008521.1|CK008521
EST:     AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAG                         GACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG
genomic: AACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACG

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: 39 (upstream exon), 75 (downstream exon)
Score: 3

ATCTTAGGCTTTATCATATTGCTCTGCGTTCTGCTGTTGGCTATATATAAAACAAATCAACCACAGCCACTTGTCAAAGGATCCGATAAGCCAGTGCAAGgtatgtgtgc ... tcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACGAGGACATCATGAGGCTGACAGAGAATTTGAGCGAGAAATACATCATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaagtatgctggcataatggaattcatcttaaccttttcttaatcatattcagGACCTCCAAAGCTAGTTGTTCTCCAGATGGACATGGCTATCCATACTTACGAGGACATCATGAGGCTGACAGAGAATTTGAGCGAGAAATACATCATTGG
                                    ttttcttaatcatatt  TA-rich tract