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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 7
gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgt-tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
||| || |  | | | ||| |  | | | | || ||  |||      || | |||| |||    |  | | ||| |     |||  ||| |||| ||||   ||||||||| ||||| || ||||||||||| || ||||||||| ||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||||
gtatgttattgctctagtttt--tcagtgtcttttcattgcccctgtcaatagaatgttttaacttcaattttagtg----atgcgcttcttgtgtttatacaagGTGGTACGCAAAACGATTTTTGCATCCCGACGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAACATTTCAATGCAGAG

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G119725_T04 (Zea mays), 3'ss of exon 7
gtaggtaaaggttattgttattat-taatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
||| |  |   ||  ||| |||||  ||| | || |   |||      || |  ||| |||    |  | | ||| |  |||   | |||||   ||||   ||||||||||||||| || ||||||||||| |||||||||||| ||||||| ||||| ||||||||||||||||| |||||||| ||||||||||| ||||||
gtatggtagtattgctgtaattatacaatgtctttttattgcccttgtcaatataatgttttgacttcaattttattgatgtg-attcttgtg--tttatacaagGTGGTATGCAAAACGATTTTTGCATCCCGATGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAGCATTTCAACGCAGAG

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaa-gtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
                    ||| | || || |   | | | |  |   |  | || ||||  | | | || || || |   ||   ||  | |||||  |  |||||||| || ||| ||||||||||||||||||||||  |    ||||| |||||||| || |||||||| || || || || |||||||||||||| || 
-------------------gttagtcatctggt-catttaccgg-ttattaagtatgtttgtcgagtatgtttttat-cgaaattctctactggttttggc--agGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtaa----aggttattgttattatta-atatgttatctgtgctga-atccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
||| | ||    |  |    || |  |  | |||   ||  | | || | |  |||   ||||| | ||   || || | |   ||     |  ||||  | |     ||||||||||||||| | ||||||||||||||||||||  |    ||||| || ||||| || |||||||| || || || || ||||| ||||||||||| 
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttat-ctacaaaatcctcaccttg-----agctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtaaaggttattgtta-ttattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
| ||  | | |  ||| ||   ||     |   | | | ||||| |   | || |||  ||  |||      |||      ||  | |   | || || |   ||||||||||||||  |||| ||||||||||||||||||||    ||||| || || || || |||||||| ||||||| |||  |||| ||||||| ||||
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagtt-aatactttttgtcctagtttatattcatagattcccat-gtattgc---agGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 7
-gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
  |   || |             | ||||   |    |||  | | |  ||||   |||||| | |         ||  | |   |  ||||| |  |     ||||||||||| |||||||||||||| || ||||| || || |  ||||| ||||| ||||| ||||||||||| || | | |   |||||| ||| |  ||
tctgattagacacccgatccgacaataattcctggcttgtttttattttattt---tttttgttttcggaatcggat-ttattgattattgtt-tgctgttatagGTGGTATGCCAAGCGGTTTTTGCACCCCGATGTAGTGGCGCCGTATGAGTACATCTTCATTTGGGATGAGGATCTTGATTTGAGGCATTTTAATCCTAAG

upper sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgtt-----ttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
      |    |  |||||| |  |  |   || ||  | |||| | |||||     | |||| ||  |||  | |  ||||  ||  || | ||       |    ||||||||||  ||||| ||||||||||||||||| || || |  ||||| || || ||||| ||||||||||| || | | |    |||||||||||   |
------atgcctgtttgttacttgtggtggattctcaat-ctgactacatttctggctctgctctgttgtcgaagt--tgtagttaactgattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG

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|88360895|gb|CI625201.1|CI625201
EST:     GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTG                         GTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
genomic: GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTGgtaggtaaag ... tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
EST: gi|428279|gb|D24427.1|D24427
EST:     GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTG                         GTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
genomic: GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTGgtaggtaaag ... tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTG                         GTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
genomic: GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTGgtaggtaaag ... tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
EST: gi|86906524|gb|CI294647.1|CI294647
EST:     GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTG                         GTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA
genomic: GAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTGgtaggtaaag ... tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTA

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: 73 (upstream exon), 59 (downstream exon)
Score: 27

CTATCATGCTATTCCATTATGATGGCCGGACTACTGAATGGGATGAATTTGAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCAGGAAGCAGACTAAGTGgtaggtaaag ... tttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
                    tcttaat  putative branch site (score: 27)
                                            ttttacct  putative PPT
                    tcttaata  TA-rich tract