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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcccttcaatttgtatagcacgatcatcatggcatgttgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG

Basic information

species Oryza sativa
transcript LOC_Os05g03820.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 10
gtttgcccttcaatttgtatagcacgatcatcatggcatgt-tgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
|||| | |||   | | | ||       |||  |||||| | || || ||  |   || || ||||||| ||||| || | |||||  |||||||||||||| | ||| |||| || ||||||||||||||||||||||||||||||||||||||||||||  |||| | |||||||
gtttactcttttgtctcttta-------catgttggcatatgtgccattgc-taggtattgcaataact-tttgtcctct-gtattctgcttgcagGTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
gtttgcccttcaatttgtatagcacgatcatcatggcatgt-tgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
|||| |||||  || ||| ||       ||  ||||||| | || |  ||  |   ||  | ||||||| ||   |||| || |||  |||||||||||||||| ||| | || || |||||||||||||||||||||||||||||||||||||||||||| ||||| | |||||||
gtttacccttttatctgttta-------cacgatggcatatctgtcgttgc-taggtatcgcaataactcttg--tcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G01750.2 (Glycine max), 3'ss of exon 10
----------gtttgcccttcaatttgtatagca-cgatcatcatggcatgttgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
           || |     ||||||   | | | |  |     ||  ||       | | |   |   |||  |    | ||||  |    ||||    || ||||| ||||||||| ||||| | |||||||||||||||||||| || || ||||| || || |||||||| |||| |||||||
gttagtttctattggtttcacaatttaactggtatctgttgctttgcaatagatttgcagcactttccttgttgtg-taacttgtgttacattattc--ttttcagGTCAGGCTGAAGAGATATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGGTTATGTGCTTTACCAGCATTTTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
gtttgcccttcaatttgtatagcacgatcatcatggcatgt-tgacactgtat---gcttaatgtaataactat-ttgttcttttgta------tttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
||| |   ||| ||| || |  ||   | | | ||| || | |  |  || ||     ||   | | |  |  | ||||  | |||||      | |   || ||||| ||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| |||| |||||||
gttagt--ttctattggtttcacaattttaac-tggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
gtttgcccttcaatttgtatagcacgatcatcatggcatgttgacactgtatgctt----aatgtaataac-tatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
                ||||||     | |        || ||| | | |||  ||     ||||  | || ||     | | || | |||  | | ||||| ||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || ||||||||||||| |||||||
----------------gtataggcacctgagatcaaattgatgaaattttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 3'ss of exon 10
gtttgcccttcaatttgtatagcacgatcat-catggcatgttgacactgtatgcttaatgtaata-----actatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
 || |    |    || ||||      |    | ||   || |    ||||| | ||||||| | |     ||   ||| | |    | | |    ||||||| ||  |||| || ||  |||||||||| || ||||||||||| |||||| |  |||||||||||||||| | ||| |||
cttcgtaacttggcttctatatggtttttggacttgtggtgatcctgctgta-ggttaatgttacataggtacggattgatatgacttctctttgctgcagGTGAGATTGAAACGGTACTTAGAGATGAGGGGAGCTGATGGTGGTCCATGGCGCCGATTGTGTGCTTTGCCTGCATTCTGG

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------------------------------------------------------------------gtttgccc--ttcaatttgtatagcacgatcatcatggcatgttgacactg-tatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
                                                                                                     ||||||   | | ||  | |  |  |||  |  |    | |||    ||     | | |||||      | ||| |      |  ||     |||||| ||||| || || ||| | |||||||| || ||||||||||| |||||| |  |||||||||| ||||| | |||||||
gtttctagtcattttgtatttcccgtctaatctttgaatacatggataattatagtgagcaatgctcgattctacaagaaatctcttaccattgtactgaattgcccggcttatttattgtgtctagatt-tgtttcagtcttgctgttggcggacattatgtacgtgtaaattgatggagcatcatttttccgcagGTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGG

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|88723315|gb|CI746825.1|CI746825
EST:     ATATTTCCTGAG                         GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: ATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|11442624|gb|BF430527.1|BF430527
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|2311262|gb|C27417.1|C27417
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|58663354|gb|CK052040.1|CK052040
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|58695197|gb|CK083884.1|CK083884
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|218498945|gb|FG948066.1|FG948066
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCTTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|58663415|gb|CK052101.1|CK052101
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|33676123|gb|CF304362.1|CF304362
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG                         GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACGATATTTCCTGAG                         GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGG

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: 66 (upstream exon), 70 (downstream exon)
Score: 65

GATTTTATGGTAGGAAAACTCCCACAAGCTCCGGGGGAGCTGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAGgtttgccctt ... tggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG
                    taataac  putative branch site (score: 65)
              ttaatgtaataactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcccttcaatttgtatagcacgatcatcatggcatgttgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT