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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccacaatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G086489_T01 (Zea mays), 3'ss of exon 13
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
                     ||      | |  | ||  || | |    |||||   ||     |||| |  | ||| |    |  ||| ||| || ||  || |  |    |  || | |||   ||||  |||| ||    |||||||| ||||| || |||||||| || || | |||||||||||||||||| ||||| ||||| |||||| ||||||| ||||
--------------------gtaggctcttgtaaaaattccttttttggtcattga--gctccagcaataacgaagttcct---aatagtctgatttgttattctttgatttgatcatatgcttgacagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTA

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G411448_T01 (Zea mays), 3'ss of exon 2
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
                      |   || |  |      |  ||  || | ||| || ||||| || | |       |||||  |  ||| | | || ||  || |  |    |  || | |||  |||||  |||| |||   |||||||| ||||| || |||||||| || || | |||||| ||||||||||| ||||| ||||| |||||| ||||||| ||||
-------------------ccaagtcctgtgacgcggcgttcctcgatggaatt-ccagcaataacgaag-------ttcct--aatagtctaatttgttattctttgatttgatcatatgcttgatagAATACAATTCCACTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTTGTGAGACAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTA

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G104294_T01 (Zea mays), 3'ss of exon 13
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
||  | |       | || || |||||| | | |    ||     | ||| ||| || ||||  ||||       | || |  || |||| ||| |||||  || |  |    |  || | ||| | ||||  |||| ||    |||||||| ||||| || |||||||| || || | |||||||||||||||||| ||||| ||||| || ||  ||||||| ||||
gtaggctct-----cgaagta-aactct-tttgtgggcattaagctcttgaattaccagcaacaacaa-------gctttc--caacagtctgatttattattctttgatttgatcatatgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G480134_T01 (Zea mays), 3'ss of exon 3
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA-----------------------
                                             |  || ||| || ||||| || | |       |||||  |  ||| ||| || ||  || |  |    |  || | |||   | ||  |||| |     |||||||| ||||| || ||| |||| || || | |||||||||||||||||| ||||| ||||  |||||| ||||||| ||||                       
-------------------------------------------gctcctgaatttccagcaataacgaag-------ttcct--aatagtctgatttgttattctttgatttgatcatatgcttgacataatacaattcttctggaatatagCGAAGAATGCAGCCGGGCTCCCATCTTTGTGAGGCAGTCAAATTTCAAGTTACCTGATGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGAG

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G377451_T01 (Zea mays), 3'ss of exon 10
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
||  | | |||||| |||||    || | |    ||  | |||     || ||| || ||||| || | |       |||||  |  ||| ||| || ||  || |  |    |  || | |||   | ||  |||| |     |||||||| ||||| || || ||||| || || | |||||||||||||||||| ||||| ||||  |||||| ||||||| ||||
gtaggct-cttgtaaaaattc---ctttttggtcattgagctcc----tgaatttccagcaataacgaag-------ttcct--aatagtctgatttgttattctttgatttgatcatatgcttgacatAATACAATTCTTCTGGAATATAGCGAAGAATGCAGTTGGGCTCCCATCTTTGTGAGGCAGTCAAATTTCAAGTTACCTGATGATCCGTCCACTCCTATTA

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|27577335|gb|CB000030.1|CB000030
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|58666486|gb|CK055172.1|CK055172
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|163926612|gb|EG713628.1|EG713628
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|29674048|gb|CB670323.1|CB670323
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCA-TTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|58681936|gb|CK070623.1|CK070623
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|58673422|gb|CK062108.1|CK062108
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
EST: gi|27576047|gb|CA998741.1|CA998741
EST:     CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAG                         AACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT
genomic: CTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 117

GATGGCTCCTTCCAGAATTCATGTAACATGTGCGTTAGTTTATGGACCTACACCAACGGGAAGGATTCACCAAGGAGTTTGTTCGACATGGATGAAGgtgagtttct ... tactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggtttcctacagcagtttgacttattcctcctccacaatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
                 gtttgac  putative branch site (score: 117)
                                           tctacttt  putative PPT
                                       aatatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccacaatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT