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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_Os02g19510.2
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
                    tcttaat  putative branch site (score: 3)
                                            ttttacct  putative PPT
                    tcttaata  TA-rich tract