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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaattaaaaaactgcttcctcatgcacatttcctatcagtttttgccttcatgtattatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT

Basic information

species Oryza sativa
transcript LOC_Os01g56670.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G171057_T01 (Zea mays), 3'ss of exon 1
gtaagcaattaaaaaactgcttcctcatgcacatttcctatcagtttttgccttcatgtat-tatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTT-ACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT
                     |  |  ||   ||||| ||  |  | |  || | ||| |  |||||  |||  ||||   |  |||||| ||||||| || |||||||||||||||||||| ||| || |||||||||| ||||| |||||| ||||||||||||||||||||||||| ||||||||||
---------------gtaagatatttgtgtgtatttcatacaatctgtcaccattatggacctatcaccattcatgaaatttgcttcattgaacagATCGATTCTTTGGATACCTTGGCTTTTACTGGGTGATAAGGAGAAATTTGGTGCTGCTGTGGAGTGGGTTGGTAAGAATGTCCACTTTGATATT

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 2
-----------gtaagcaattaaaaaactgcttcc---------tcatgcacatttcctatcagtttttgccttcatgtat-tatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT
            |  |   |||        ||            |  ||   ||||| ||  |  | |  || | ||| |  |||||  |||  ||||   |  |||||| ||||||| || ||||||||||||||||||||||| || |||||||||| ||||| |||||| ||||||||||||||||||||||||| ||||||||||
gtgaagactcccttggtggttatgcgctcactcttgtaagatatttgtgtgtatttcatacaatctgtcaccattatggacctatcaccattcatgaaatttgcttcattgaacagATCGATTCTTTGGATACCTTGGCTTTACTGGGTGATAAGGAGAAATTTGGTGCTGCTGTGGAGTGGGTTGGTAAGAATGTCCACTTTGATATT

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020359_T02 (Zea mays), 3'ss of exon 2
gtaagcaattaaaaaactgcttcctcatgcacatttcctatcagtttttgccttcatgtat-tatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT
                     |  |  ||   ||||| ||  |  | |  || | ||| |  |||||  |||  ||||   |  |||||| ||||||| || ||||||||||||||||||||||| || |||||||||| ||||| |||||| ||||||||||||||||||||||||| ||||||||||
---------------gtaagatatttgtgtgtatttcatacaatctgtcaccattatggacctatcaccattcatgaaatttgcttcattgaacagATCGATTCTTTGGATACCTTGGCTTTACTGGGTGATAAGGAGAAATTTGGTGCTGCTGTGGAGTGGGTTGGTAAGAATGTCCACTTTGATATT

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|88356084|gb|CI627532.1|CI627532
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88692969|gb|CI736544.1|CI736544
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCCTTTACTAGGGGATAAGGAGAGATTTGA
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGC-TTTACTAGGGGATAAGGAGAGATTTGA
EST: gi|88761662|gb|CI771218.1|CI771218
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88579110|gb|CI688081.1|CI688081
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAG
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAG
EST: gi|88315165|gb|CI611829.1|CI611829
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGGTTGACTAGGGGATAAGGC-AGATC-GAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88738554|gb|CI762062.1|CI762062
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGG
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGG
EST: gi|88404794|gb|CI583601.1|CI583601
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88315352|gb|CI613621.1|CI613621
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88584472|gb|CI702027.1|CI702027
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATT
EST: gi|29678673|gb|CB674948.1|CB674948
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88740319|gb|CI763827.1|CI763827
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGA
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGA
EST: gi|88452946|gb|CI574493.1|CI574493
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88726361|gb|CI750016.1|CI750016
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
EST: gi|88404616|gb|CI581052.1|CI581052
EST:     CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTT                         ATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT
genomic: CTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGAT

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: 54 (upstream exon), 63 (downstream exon)
Score: 3

TGCATTTGATGGGTACATGCAACATGCTTTTCCACTTGATGAATTGCGGCCTTTAAGTTGCCAAGGAGAAGATTCACTTGGTGGCTATGCACTTACTCTTgtaagcaatt ... cattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtttttgccttcatgtattatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT
                                       cttattc  CT-rich tract
                  tattatcatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaattaaaaaactgcttcctcatgcacatttcctatcagtttttgccttcatgtattatcatgatttgtgaatgcttattcattaaacagATAGACTCTTTGGATACCTTGGCTTTACTAGGGGATAAGGAGAGATTTGATGCTGCCGTGGAGTGGGTTGGTAAGAATGTCCGCTTTGATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG