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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatatgcatctgacttacagtgatggctccttttctatttaacatatcgaccttcctttttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT

Basic information

species Oryza sativa
transcript LOC_Os03g21460.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G031825_T05 (Zea mays), 3'ss of exon 3
gttagtatatgcatctgacttacagtgatggctccttttctatttaacatatcgaccttccttttt----ggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT
|||||||||  |||||  |||| || ||||| | |||||   | | | ||    |||||  |||||      || ||||||||||||| |||||||  |||||||||||  |||||||||||||||| || ||||||  ||| |||||||| |||||||| ||| |||| | |||||
gttagtatacacatctttcttagagcgatggtttcttttggttgttatatcataacctttttttttttgaaatacagTTCATTGCTGGGTGTGGGAAGTTTTTTGAGGGTTCTGCAGAGCAAATGTATCAGTCCCTTATTGTTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTT

upper sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G14600.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------gttagtatatgcatctgacttacagtgatggctccttttc--------tatttaacatatcgaccttcctttttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT
                                                                                ||   |   |  || |   |||    || | |    |||         ||||||   | |       |    ||  ||||||| |||||||||||||||| ||||||||| || |||||||| || || || || || || ||||| ||| | || ||  | || ||||||||   |||||
gttcttaggaaagaatacaataaattgattctaaaagctatgccaagtgcttggaatctgtgtatatgacttgcctttttgtctatgcttttatgtatattatgaagaggtcctactttaaaatcctatatttattttgttattgcacgcgctttctatagTTTATTGCTGGTTGTGGGAAATTTTTTGAAGGAACTGCAGAACAGATATATCAGTCACTCTGTGTGACATTAGGTTCATTACCAAAGCCAACCAGAGTTT

upper sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0067g00180.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gttagtatatgcatctgacttacagtgatggctccttttctatttaacatatcgaccttcctttttg---gtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT
                          ||  || |   |||   ||    || | | | |  |  ||   |    || |   || |||  ||   ||  ||||  ||||||||||||||| ||||||||| ||||| ||||| || ||||| ||||| || ||||||||| ||| |||  |||| |||||||||  ||| |
aatgactggatccctttactttgtaataaaatcttgttcttttttgacttgctagttacgatgttaaacagttaatagtggttacttcatgcatgtgcagTTTGTTGCTGGTTGTGGGAAATTTTTTGAAGGCACAGCAGAACAGATGTATCAATCGCTATGTGTAACATTGGCCTCATTGCCAAAGCCAACTAGAGTAT

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|33687222|gb|CF315461.1|CF315461
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|33687113|gb|CF315352.1|CF315352
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|33808256|gb|CF330017.1|CF330017
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|87022853|gb|CI269789.1|CI269789
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTCGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|33654738|gb|CF277352.1|CF277352
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|218494169|gb|FG952751.1|FG952751
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|2443021|gb|C74792.1|C74792
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|86599871|gb|CI256033.1|CI256033
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|66913473|gb|CX100321.1|CX100321
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|33659109|gb|CF281722.1|CF281722
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|88762168|gb|CI771724.1|CI771724
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
EST: gi|33661942|gb|CF292909.1|CF292909
EST:     TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTG                         TTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC
genomic: TCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTAC

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: 71 (upstream exon), 73 (downstream exon)
Score: 40

CCACACAAAAGGACATATCAGCTATTACGTCACTAGTAAAGAGGAGGAAGATCCAGCAGTGTTTACTGGAGACACCTTGgttagtatat ... tttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacagtgatggctccttttctatttaacatatcgaccttcctttttggtatagTTCATTGCTGGTTGTGGGAGATTTTTTGAGGGCACTGCAGAGCAAATGTACCAATCCCTTTGTGTAACACTGGGCTCGCTGCCTAAGCCAACTCAAGTTT
                       atttaac  putative branch site (score: 40)
                                 tcgaccttccttttt  putative PPT
                 ttttctatttaacata  TA-rich tract