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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA

Basic information

species Oryza sativa
transcript LOC_Os02g33580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G100766_T01 (Zea mays), 3'ss of exon 1
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcatttcatcatctgtgtt-taccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
             ||  || | | | |      |   || |    | || ||  | | |        ||||| |||| ||| || | ||    |    |||||  |  ||| ||||||||||| ||||  || |||||||| ||||||||||| |||||| |||||||  | ||||| || |||||||| ||||| |||||||| || ||||||
-------------aaacaagaaactttaaggcaattgtcaaagataattaattctgtattccactttttttgttgattactaatgctgccatttgctgtttgtatt-tttttagGTACAAGGTTTTCAAAAATCCGAGCATTAGTGATGTCCTATGCACAACAACAGCATAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA

upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
gtatgtatcactcaagaaaaac--agtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
||| ||||||  |||||||     ||     | |||      || | |||   |  ||    |||   ||||| |||| |||||| | ||    |    |||||  |  ||||||||||||||| ||||| || |||||||| ||||||||||||||||||||||| || || ||||| || |||||||| ||||| |||||||| || ||||||
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataat-taattctgtattccactttt---ttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA

upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G002043_T02 (Zea mays), 3'ss of exon 8
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
||| ||||||  |||||||      | ||  |     || |    | || ||  | | | |     ||||| |||| |||||| | ||    |    |||||  |  |||||||| |||||| ||||  || |||||||| |||||||||||||||||| ||||||| || ||||| || |||||||| ||||| |||||||| || ||||||
gtacgtatcaaacaagaaactttaag-gcaattg---tcaaagataattaattttgtatttcacttttttgttgattactgatgctgccatttgctgtttgtatt-ttttcagGTGCAAGGTTTTCAAAAATCCGAGCATTAGTGATGTCCTGTGCACAACAACAGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA

upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G037789_T01 (Zea mays), 3'ss of exon 1
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctacttt-cagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
            ||| ||    |  |   |          |  | |||   |  ||    ||    ||||| |||| |||||| | ||    |    |||||  |  ||| |||||||||||| ||||| || |||||||| |||||||||||||||||| |||||   || |||||  | |||||||| ||| | ||||||||    ||||||
----------tgcaacaagtttaaggcaattgtcaaagataattaattctgtattccacttt----ttttgttgattactgatgctgccatttgctgtttgtattttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAACAACAATAGAGGCTCTTTCAATGGGGAAATTCATGATCTGCGCAAGACATCCA

upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcattt-catcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
                                 | ||||   |  || | | |    | |    || | ||   | |      |     || |||||     |  |  |   |||||||| || ||||| ||||| |||||||| ||||| || ||||||||||| || ||||| || || ||||||||||| ||  | || || || || || 
-------------------------------gtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtctttcccacatcttgatga-agGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT

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|29678871|gb|CB675146.1|CB675146
EST:     ACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
genomic: ACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
EST: gi|29673409|gb|CB669684.1|CB669684
EST:     GGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
genomic: GGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
EST: gi|218505479|gb|FG952711.1|FG952711
EST:     CCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
genomic: CCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
EST: gi|29678872|gb|CB675147.1|CB675147
EST:     AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATNCA-CCCGAGCATCAGTGATGTCCTGTGCACAGCAA
genomic: AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCAT-CAACCCGAGCATCAGTGATGTCCTGTGCACAGCAA
EST: gi|29678873|gb|CB675148.1|CB675148
EST:     TTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
genomic: TTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAAC
EST: gi|29678870|gb|CB675145.1|CB675145
EST:     AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATNCA-CCCGAGCATCAGTGATGTCCTGTGCACAGCAA
genomic: AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCAT-CAACCCGAGCATCAGTGATGTCCTGTGCACAGCAA
EST: gi|11442630|gb|BF430533.1|BF430533
EST:     AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGG                         GTACAAGGTATTCATCA
genomic: AATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCA

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: 69 (upstream exon), 70 (downstream exon)
Score: 33

GTGGCGAGGACTCACAAGAAGTCCAATCTACCGCCAAGAAACTGAACCTGAATCTAAACTTTTTTAAGGGAAGGGACCATGCAGATGACTCACTCCATGGgtatgtatca ... ctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
                  cactgat  putative branch site (score: 33)
                                cctttcttttgtgcta  putative PPT
                                  tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA