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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtagatgtacttgtatgcaggctggattaatttccagtagaacaaagatagaattcacgatgcacatttttgtggtaagctatacatcctcatgcttaatttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAGAACACTTTCTTTGCTGACCTGTGCTACACAAAGTGGGCTCTAGAAGGGT

Basic information

species Oryza sativa
transcript LOC_Os11g22350.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g22350.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G064603_T01 (Zea mays), 3'ss of exon 9
gtgagtgttgtagatgtacttgtatgcaggctggattaatttccagtagaacaaagatagaattcacgatgcacatttttgtgg-taagctatacatcctcatgcttaatttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAGAACACTTTCTTTGCTGACCTGTGCTACACAAAGTGGGCTCTAGAAGGGT
                               ||  | |    || || |    || || |   ||  |||| |    |   ||  | | | | ||||    || |            |||||||| ||  |||||||||| ||||||||||||||||| ||||||| |||| ||||| || |||| |||||||||||||| ||||||||||| ||||  |
------------------------------gtgagtgaggcacctgtcgtcttaatattg--ctcctgatgaatgaatgaatgaatgaacaacacatgtgtattc------------cagTGGTCGGCCTTGCTTCCGGTGGTTTTGACTCTGATAGCCACTCAGCAGAAGGACACTATCCTTGCCGACCTGTGCTACACCAAGTGGGCTCTGGAAGCCT
















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|29675381|gb|CB671656.1|CB671656
EST:     GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|88966309|gb|CI119444.1|CI119444
EST:     GGCTACACGTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: GGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|88259346|gb|CI363639.1|CI363639
EST:     GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|87029848|gb|CI274529.1|CI274529
EST:     CACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: CACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|88258590|gb|CI361176.1|CI361176
EST:     TCGG-TACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGTTCCTTTTGACTCTGATAGCAACTCAGC-GAAG
genomic: TCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|86480362|gb|CI122995.1|CI122995
EST:     GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|88255082|gb|CI353906.1|CI353906
EST:     TCTTCTTTCAGGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: TCTTCTTTCA-GCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
EST: gi|86479534|gb|CI122167.1|CI122167
EST:     GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTG                         TGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG
genomic: GCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAG

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: 74 (upstream exon), 66 (downstream exon)
Score: 4

CATCTGGGAGAACTACGTCATTCTTGTTGCCCTCGTCTACTGCGTCACTGGCATCGGCTACACTTTCGCCATCTTCTTTCAGCCAGGCTCTGCACAGTTGgtgagtgttg ... ttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAGAACACTTTCTTTGCTGACCTGTGCTACACAAAGTGGGCTCTAGAAGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgatgcacatttttgtggtaagctatacatcctcatgcttaatttctgtgcagTGGTCTGCGCTGCTTCCGGTCGTTTTGACTCTGATAGCAACTCAGCGGAAGAACACTTTCTTTGCTGACCTGTGCTACACAAAGTGGGCTCTAGAAGGGT
                                      gcttaat  putative branch site (score: 4)
                                            tttctgt  CT-rich tract
                                        ttaatttct  TA-rich tract