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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggctataattttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttttgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG

Basic information

species Oryza sativa
transcript LOC_Os04g40874.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
gtaatggctataa--ttttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttttgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG
||||||| | |||  |||||||||     | |  | |  |    | |||||||| |||| || |||| || ||||  ||| ||||||||||| ||||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||
gtaatggatgtaacattttgtcaac----ttgctttacatttcacaaatacttgtctaattattttttaaccaatatcatgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 6
gtaatggctataattttgtcaagaatgtgggatgatttcctccgaatacttgac-taactacttttgaaacaa-tcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG
||| |    || |||   |   |  | |   ||   || || |  | ||||| | |||   || |  |    | | | ||| | ||| | || ||||||||||| ||||| || ||| ||||||| |||||||||||||| |||| |||| | |||
gtagtaa--atgattgcttattggctctcatattgcttgcttcataaacttggcctaatccctctccatttgacttgtattac-cagTTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAG

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgg----ctataattttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttttgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG
||||       || || |  |||| | |   |       |||| |  || ||   |  | | || ||||    |   |   | |  ||| | || || || ||||| || ||||| |||||||| |||||||||||||||||||| || ||  | |||
gtaacctgcttctctattaatgtctaaatcatcaatctctttctttagactatcag--tgatta-ttttatctcgtgcatttcttgcagTTGGTCCTCCGGTTTGCAAATCGCTTTTTCTTGCCACTTTGGAACCGTGACAATATCGAGAACGTGCAG

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------gtaatggctataattttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttt---tgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG
                                          ||     |||||    |        | | |||   |  |  |||   |   || | | || |   |    || |  |||||  ||| | || ||||||||||| || ||| |||| ||||| || |||||||||||||| ||||||||| |||||
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacattt-gcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG

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|29663317|gb|CB659592.1|CB659592
EST:     AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
EST: gi|86850539|gb|CI307768.1|CI307768
EST:     AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
EST: gi|29614696|gb|CB619709.1|CB619709
EST:     AACTCTACAGAATTGATCACTACTTGGGGAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
EST: gi|29680803|gb|CB677078.1|CB677078
EST:     AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
EST: gi|88456177|gb|CI565827.1|CI565827
EST:     AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGAC
EST: gi|117243651|gb|CT843162.1|CT843162
EST:     AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCCAACCGCTT
genomic: AACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTT

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: 67 (upstream exon), 69 (downstream exon)
Score: 72

CTCTGCAGAAGAATTAAGTGCCCAACTTGGGGAGCTATTTGACGAAAACCAACTCTACAGAATTGATCACTACTTGGGAAAAGAGTTGGTCCAAAACCTGgtaatggcta ... catttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatttcctccgaatacttgactaactacttttgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG
                     gactaac  putative branch site (score: 72)
                               ttttgaaa  TA-rich tract