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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatggcatgcataccggttagccatctcctttgtactgccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G398107_T01 (Zea mays), 3'ss of exon 3
gtga---atgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatggcatgcataccggttag-ccatctcctttgtactgccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
|| |   ||||  | |   | ||| || |  ||   ||  | |||     || | |    |   |  | | | | ||| |      |     |||  |     | |||||| |||     |||  ||| |  |                 | ||| ||||| ||| | ||||||||||  |||||||| || ||  | ||||||||||||| |||| | |||||||||||||||||||||||||||||||||||||| |||||||| |
gtaagttatgaactttatgtgattgta-atattttgattttatgtggtcaaatatatggaccgacacggtcc-gatgaaggcacggt----gtggtttaggaccgggttaggccactgtttttacacttcgga----------------ctgacacaaagtgacaagctgtttatggttctcagGTTACATAGGCCCGGTTTCCTTTTTAAATACTATGCTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGACCTTGTATACG

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 5
gtgaatgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatg-gcatgcataccggttagccatctcctttgtactgccaaata-aggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
                                                                                  |   ||||    ||  |||    |           | | ||     | ||| |  | |          ||| ||||| ||||| ||||||||||  ||||||||||| || || ||||||||||||  |||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||
----------------------------------------------------------------------------------actgcaatatatatatatatatatatatatatatatatatatatatatatatatatatacacacacacacacaaagtgacatgctgtttatggttctcagGTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG
















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|88580749|gb|CI697698.1|CI697698
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTAC
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTAC
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88339276|gb|CI633847.1|CI633847
EST:     CGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATGGGATCTGTTTCCTTTTCAACTACTGTACTACAAGT
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGT
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88355870|gb|CI625499.1|CI625499
EST:     TGAAGGGGTGGGGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTCTAACTACTGTACTACAAGTTG
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTG
EST: gi|88341926|gb|CI644263.1|CI644263
EST:     TGAAGGGCTGGCGGAAAACGATCTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTACCTACTGTACTACAA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAA
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAAC
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAAC
EST: gi|88337186|gb|CI628272.1|CI628272
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTT-AACT
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACT
EST: gi|58661072|gb|CK049752.1|CK049752
EST:     TGAAGGGCTGGTGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTCAACT
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACT
EST: gi|88385774|gb|CI566636.1|CI566636
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTACCTACTGTACTA-AACGTTGTTGAC
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAA-GTTGTTGAC
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA

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: 61 (upstream exon), 51 (downstream exon)
Score: 17

CCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
                            aagtaac  putative branch site (score: 17)
                  ttttaacaaaaagtaa  TA-rich tract