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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctatataaccattcctttttttattatttttcatgctattgtagagattgaagtgccactaactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC

Basic information

species Oryza sativa
transcript LOC_Os07g01930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G013607_T06 (Zea mays), 3'ss of exon 1
----gtatgctctatataaccattcctttttttattatttttcat-gctattgtagagattgaagtgccact---aactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
          ||||     || |   ||| ||     ||| | || | |    | || |||  |||  ||||   |||||    |||   | || ||||||||||||| |||||||| ||| ||||||||||| ||||||||||||| ||||||||||||||||||||||| || ||||||||
tctctagcagtctaacctgccctaattttcttggggttttgttattgttgccattgatattctagtttcactgctaactacaattttttgtcttatccagGATGTAAAATATTATAACAAGTTAGAAGATCCAGCAGATGAAGAAAACGATATGCTTGACCTTGCATTTGGGCTCACAGAAAC

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G856338_T01 (Zea mays), 3'ss of exon 2
-gtatgctctatataaccattcct-----ttttttattatttttcatgctattgtagagat----tgaagtgccactaactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
 || |   |    | |   ||| |     | | || || || ||   | |||| |||   |      || ||| |||   ||   ||||  || || ||||||||||||| || ||||| ||  ||||||||||| ||||||||||||||||||||||||||||||||||||| || ||||| ||
agtctaacccgccttaattttcttggggttatgttgttgttgttgccgatattctagttttgctgctaactgcaactttttaa--atttttatcttatccagGATGTAAACTACTATAACAAATTAGAAGATCCAGCAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGGCTCACAGAGAC

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G05450.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgctctatataaccattcctttttttattatttttcatgctattgtagagattgaagtgccactaactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
            ||| |||   || ||  ||||||  |      || | |     ||   | ||   ||||||| |      | || | ||||||    | || ||||| || || ||||| |||||||||||||| |||||||||||||| ||||| ||||| || ||||||||
-----------gtaaacat--attcttccattattaatag----atcgaatcctctgcttttccggaaactagctaagattgtatt-tacagGATACTGAATACTATAACAAACTTGAAGAACCAACAGATGAAGAGAATGATATGCTTGATCTTGCTTTTGGGCTCACAGAAAC

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ35997 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctctatataaccattcctttttttattatttttcatgctattgtagagattgaagtgccactaact--agccatttcaattttgtcca--gGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
                                                   | || |   | |   |  ||  ||| |||   || | |  ||  |||||  || | ||||   | |||  | || ||| | || || || ||||| |||||||| |||||||||||||||||||| ||
-------------------------------------------------gtatatcgtcttccttttttcttgagcgattcgtatgtggatcacagGATGAGAAGTTTTATCGGATGCTCAAGGAGCCATCGGACGAGGAGAATGACATGCTTGATCTTGCATTTGGACTTACAGAGAC

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ36222 (Selaginella moellendorffii), 3'ss of exon 3
gtatgctctatataaccattcctttttttattatttttcatgctattgtagagattgaagtgccactaact--agccatttcaattttgtcca--gGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
                                                   | || |   | |   |  ||  ||| |||   || | |  ||  |||||  || | ||||   | |||  | || ||| | || || || || || |||||||| |||||||||||||||||||| ||
-------------------------------------------------gtatatcgtcttccttttttcttgagcgattcgtatgtggatcacagGATGAGAAGTTTTATCGGATGCTCAAGGAGCCATCGGACGAGGAGAACGACATGCTTGATCTTGCATTTGGACTTACAGAGAC

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|33796313|gb|CF324024.1|CF324024
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|88261690|gb|CI365266.1|CI365266
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|88288335|gb|CI515479.1|CI515479
EST:     GTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|10794608|gb|AU108574.1|AU108574
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|218490073|gb|FG948574.1|FG948574
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAA-AAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|66917010|gb|CX103858.1|CX103858
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|33680136|gb|CF308375.1|CF308375
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|24468825|gb|CA305774.1|CA305774
EST:     GAGCATGTGAAGGTTCACCTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|88304282|gb|CI515555.1|CI515555
EST:     TGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: TGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|33680135|gb|CF308374.1|CF308374
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
EST: gi|11443010|gb|BF430897.1|BF430897
EST:     GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATG                         GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT
genomic: GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGAT

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: 50 (upstream exon), 72 (downstream exon)
Score: 8

GAGCATGTGAAGGTTCACTTGCGTGTTCAACCTGTCATGTCATAGTTATGgtatgctcta ... ttttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgctattgtagagattgaagtgccactaactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC
                          cactaac  putative branch site (score: 8)
                                             ttttgtcc  putative PPT
                                      atttcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctatataaccattcctttttttattatttttcatgctattgtagagattgaagtgccactaactagccatttcaattttgtccagGATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA