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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA

Basic information

species Oryza sativa
transcript LOC_Os12g03720.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 10
gtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttcc-ttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA
         |||| | |   | ||  |||      | |||    | ||   || |  |||  ||  | |    ||||||    |||||| |  |||||||||| ||   ||||| ||||||| ||||||||||| ||||| || ||||| || || || ||||||||||||||||| ||||| ||||| || || |  | || ||    |   |
-------gtttgtctaa---gcttggtttgtgtggagtccgt--cctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcagTTGCTCGCGTACCATCTGACTGTTCTCCGGGGATTCGACGTGGACCAACCAAGGAATCTGGCGAAGAGCGTGACCACGCAGTAGGGAGAGGTAGATGAGA

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctac-ttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA
             |  |||| || |  |  |    | || | ||  | |   || |  ||| || |||  ||     |||    |  |   | | || || ||  |   | ||| || | || || |||||||| ||| |  ||||     ||||||||||||| |||||||||||||||||||||||||| ||||                  
------------gtaaaattcttaacctctaaatcaatctataatctatgtatttttttttttcgttttcgacgtg-tttatggtgttttttttcttcttcttcttgggtacagTTGTTGGCTTATCATCTGACTGTTTTGAGAGGTCACAATGTTGATCAACCGAGGAATCTGGCAAAGAGTGTGACTACTCAATAG----------------

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 3'ss of exon 10
gtttgcacattgtttgaattgtttaatttcatcaaattccag--aacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgt-attgttatttgttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA
                      || |||||   ||  |  ||  | |||||||   |   || | |        |   | ||| ||| |   ||| | | || | | |   | ||| || | ||||| ||||| || || || || || |   | || || |||||  ||||||| ||||||||||||||||||||||||| | ||     |   |
----------------gtcacctttatttccaaaagctggagttatcttctacagttaggttttaaacaaaattaagttgtcacttattccttgtcaatattttctttcggtgcagTTGTTGGCATATCATCTTACTGTCCTACGTGGTTACAACGTCGACCAACCTCGGAATCTTGCAAAGAGTGTGACTACCCAATGAGAAAGGTTCATTTATA

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|86426649|gb|CI071746.1|CI071746
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88485727|gb|CI422998.1|CI422998
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88902738|gb|CI088276.1|CI088276
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88849760|gb|CI089866.1|CI089866
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|58600045|gb|CK010573.1|CK010573
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86479812|gb|CI122445.1|CI122445
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|89184705|gb|CI007130.1|CI007130
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88434918|gb|CI549115.1|CI549115
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|87026077|gb|CI250093.1|CI250093
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86834864|gb|CI345948.1|CI345948
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88837681|gb|CI079041.1|CI079041
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|3766919|gb|AU031029.1|AU031029
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88251227|gb|CI349655.1|CI349655
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86496093|gb|CI138726.1|CI138726
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86599332|gb|CI355949.1|CI355949
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAA                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86481498|gb|CI124131.1|CI124131
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|38481981|gb|CF966044.1|CF966044
EST:     CTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88902955|gb|CI088493.1|CI088493
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86833049|gb|CI333648.1|CI333648
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88251266|gb|CI349694.1|CI349694
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA

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: 74 (upstream exon), 46 (downstream exon)
Score: 7

AGACGCATCTGCAGTTTGCCCTAGTGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA
                                       ttatttgttccttc  CT-rich tract
            aaacaatttcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcacattgtttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtattgttatttgttccttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG