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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccatgcttagaaagtattctagaatcaattttgaaatggcctttctgatggtatatatatttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 8
gttagtccatgctta-----gaaagtattctagaatcaattt--------tgaaatggcctttctgatggtatatat-attt-ctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG
|| |||  |   |||      | |  ||| ||  |||||||            |||    ||||||| ||    ||| |||| || |||||||| ||| ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||| |||
gtaagtttacttttattagtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG

upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 10
gttagtccatgcttagaaagtattctagaatcaattttgaaatggcctttctgat-ggtatatatattt-ctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG
|| |||  |   ||  |   ||   |   |  | |     ||     |||||||| ||  ||||||||| ||  |||| || ||| ||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||| |||
gtaagtttactgttttagtataagattttaatattgacagaacatgttttctgatcggggtatatatttacttgtagGCACCATGGTTGCATCTTCTCTAATGGACAAGCAAGGAAGGAAAAGCCTTCTGATGACAAGCTTTTCTGGAATG

upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 10
-------------gttagtccatgcttagaaagtattctagaatca-attttg----aaatggcctttctgatggtatatatat-ttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG
              |   ||     |     |  ||| |    ||| | ||||     ||||   |   |||  | || |  || |||| | ||| |||   || ||||| ||| ||||||||| |||||||||||| || ||||| |||||||||||| |||| |||
gtaatcctttttattctctctgatttcttgtaaaattttgatttcatactttgtagagaatgttttacatgactggattttgatcttcttacagGCACAGCCATAGCATCCTCTTTGATGGACAGGCAAGGAAGGAAAAGTCTTCTAATAACAAGCTTTGCTGGGATG

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|38477850|gb|CF961983.1|CF961983
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|163921085|gb|EG710424.1|EG710424
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|38481055|gb|CF965144.1|CF965144
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|7219969|gb|AU065196.2|AU065196
EST:     GCATCTGAATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAANGAAGGAANAGCCTTC
genomic: GCATCTGA-TGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|58598313|gb|CK008841.1|CK008841
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|55409376|gb|CV721752.1|CV721752
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|27554385|gb|CA998285.1|CA998285
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
EST: gi|27576947|gb|CA999641.1|CA999641
EST:     TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTG                         GTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC
genomic: TGCATCTGATGTTGCAGCGAGTGCCCTTGTTGGAGCAGCCAATGTTTTTGgttagtccat ... tttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctagaatcaattttgaaatggcctttctgatggtatatatatttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG
                            ttctgat  putative branch site (score: 3)
                                           tatttct  putative PPT
                                     tatatatatttctgat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccatgcttagaaagtattctagaatcaattttgaaatggcctttctgatggtatatatatttctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT