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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattaagagcataaactcgatggaaaataatatgccctttttttgaagttatattgacatttagggtttagtataaccaacttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------gattaagagcataaactc---gatggaaaataatatgcccttttttt---gaagttatattgacatttagggtttag-tataaccaacttatgagttttatgc-acagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG
                                                                                    | ||  | | | || ||     || ||  ||| || ||  ||    |   |||| |    | | || |      | | | | |   |   |     |||||||  |||| ||||||||||||||||  ||||| |||||||||||||| ||||||||||| ||||| || ||||| ||  ||||||||| ||| ||||| || |||||
gtgattcagccatgcctgcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 3
--------------gattaagagcataaactcgatggaaaataat---atgccctttttttgaa-gttatattgacatttagggtttagtataaccaacttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG
                | ||     |   |    || || || |    |||| ||| ||||||| | |          ||   ||| |   |     |  |  || |||||    ||||||| |||||||||||| ||||||| ||||||||||| || || |||||||| ||||| |||||||| ||| | || |||||||||||||| || |||||
gtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctg-gatttttactt-cagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG
















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|88763952|gb|CI773368.1|CI773368
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29632559|gb|CB637568.1|CB637568
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGACGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88734903|gb|CI758411.1|CI758411
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29646541|gb|CB651548.1|CB651548
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88299972|gb|CI580033.1|CI580033
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAAAGAG                         GTTTTGAAGCTGGAGGCC-TCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88740536|gb|CI764044.1|CI764044
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29673416|gb|CB669691.1|CB669691
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29638131|gb|CB643140.1|CB643140
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88745225|gb|CI768585.1|CI768585
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88735131|gb|CI758639.1|CI758639
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29680212|gb|CB676487.1|CB676487
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29674874|gb|CB671149.1|CB671149
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29681802|gb|CB678077.1|CB678077
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACACAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29634180|gb|CB639189.1|CB639189
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88737430|gb|CI760938.1|CI760938
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29628283|gb|CB633294.1|CB633294
EST:     CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA

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: 55 (upstream exon), 73 (downstream exon)
Score: 39

GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagt ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttatattgacatttagggtttagtataaccaacttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG
                     tttagtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattaagagcataaactcgatggaaaataatatgccctttttttgaagttatattgacatttagggtttagtataaccaacttatgagttttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG

- - - -agcataa
- - - - - - - -ctcgatg
- - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - tatgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatga