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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcccctttccacgtgattaacagctttaatttacatgtgaatcagagttgtggctgctctgaatctttcagcatttctaatgatctttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA

Basic information

species Oryza sativa
transcript LOC_Os12g06800.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G468799_T01 (Zea mays), 3'ss of exon 13
gttatcccctttccacgtgattaacagctttaatttacatgtgaat-cagagttg---tggctgctctgaatctttcagc----atttcta-atgatctttatttcgaaatcatgagtt--------tgta-acattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
||||| |||||| | | |    || ||   |||||||| |||| |  | || ||    | ||||| || |||  ||  ||    ||  ||| ||  || ||||| | |  |||||| ||        || | |  ||||  |  | | | ||||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||| || | ||||| |||||| |||||||| ||||||||||||||||
gttattcccttttctcatctcaaatag---taatttacttgtgtacacggaatttgttttgctgcactaaatgatttggccccaatccctatatagtccttattgc-atgtcatgacttgcgagcaatgcacatgtttttctttctttcaagGATGGCTATGTACCATATCACTCAGCGAGAATGGAGCTCTGCCCAGCCGCATCATCGGACACCTCAAAGAAGGGTCAAGTCTTCACAGAAATGCTCAACA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G163594_T01 (Zea mays), 3'ss of exon 9
gttatcccctttccacgtgattaacagctttaatttacatgtgaat-cagagttg---tggctgctctgaatctttcagcatttcta---atgatctttatttcgaaatcatgagtt--------tgta-acattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
||||| |||||| | | |    || ||   |||||||| |||| |  |||| ||    | ||||| || |||  ||  || | ||     ||  || ||||  | |  |||||| ||        || | |  ||||  |  | | | ||||||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| || | |||||  ||||| |||||||| ||||||||||||||||
gttattcccttttctcatctcgaatag---taatttacttgtgtacacagaatttgttttgctgcactaaatgatttggcctctccctatatagtccttatagc-atgtcatgacttgcgagcaatgcacatgtttttctttctttcaagGATGGCTATGTACCATATCACTCAGCAAGAATGGAGCTCTGCCCAGCTGCATCATCGGACACCTCAAAAAAGGGTCAAGTCTTCACAGAAATGCTCAACA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G039505_T02 (Zea mays), 3'ss of exon 13
gttatcccctttccacgtgattaacagct-ttaatttacatgtg-aatcagagttgtggc------tgctctgaatctttcagcatttctaatga----tctttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
||||| |||||||| | |   ||| |||  || | || | |||| |||  |  |||  ||      |     | |   |  ||   || ||        || | | ||   |   |||   |    |||  ||  ||   | ||||||||| || ||||||||||||||||| ||||||||||||||||| ||||||||||| || |  |||| ||||||||||||||| ||||||||||| ||||
gttattccctttcctcatctctaatagcaatttacttgcgtgtggaatttgttttgctgcaataaataactgggactctatagtccttatagcagcatgtcatgacttgtgagctatgccctatgcacacctttgtgttcttccagGATGGCTACGTACCATATCATTCAGCGAGAATCGAGCTCTGCCCAGCTGCATCATCGGACACGTCAAAGAAGGGCCAAGTCTTCACAGAAATGCTGAACA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G176042_T01 (Zea mays), 3'ss of exon 8
gttatcccctttccacgtgattaacagctttaatttacatgtgaat-cagagttg---tggctgctctgaatctttcagcatttcta---atgatctttatttcgaaatcatgagtt--------tgta-acattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
||||| |  ||| | | |    || ||   |||||||| |||| |  |||| ||    | ||||| || |||  ||  || | ||     ||  || ||||  | |  |||||| ||        || | |  ||||  |  | | | ||||||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| || | |||||  ||||| |||||||| ||||||||||||||||
gttattcttttttctcatctcgaatag---taatttacttgtgtacacagaatttgttttgctgcactaaatgatttggcctctccctatatagtccttatagc-atgtcatgacttgcgagcaatgcacatgtttttctctctttcaagGATGGCTATGTACCATATCACTCAGCAAGAATGGAGCTCTGCCCAGCTGCATCATCGGACACCTCAAAAAAGGGTCAAGTCTTCACAGAAATGCTCAACA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G127810_T02 (Zea mays), 3'ss of exon 4
gttatcccctttccacgtgattaacagctttaatttacatgtgaat-cagagttg---tggctgctctgaatctttcagcatttcta---atgatctttatttcgaaatcatgagtt--------tgta-acattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
||||| |||||| | | |  | || ||   |||||||| |||| |  | || ||    | ||||| || |||  ||  || | ||     ||  || ||||  | |  |||||| ||        || | |  ||||  |  | | | ||||||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| || | |||||  ||||| |||||||| ||||||||||||||||
gttattcccttttctcatcttgaatag---taatttacttgtgtacacggaatttgttttgctgcactaaatgatttggcctctccctatatagtccttatagc-atgtcatgacttgcgagcaatgcacatgtttttctttctttcaagGATGGCTATGTACCATATCACTCAGCAAGAATGGAGCTCTGCCCAGCTGCATCATCGGACACCTCAAAAAAGGGTCAAGTCTTCACAGAAATGCTCAACA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G58350.3 (Arabidopsis thaliana), 3'ss of exon 13
gttatcccctttccacgtgattaacagctttaatttacatgtgaatcagagttgtggctgctctgaatctttcagcatttctaatgatctttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
          ||||| ||  || | | ||| | | |       | |   ||   |      | | |||   | ||       | ||||  ||||||  ||  ||  | | ||    | | |  ||  || | |||| |||||||| |||||||| |||||||||||||||   ||||   |||| || |  || | ||| |  | |||    | |||    |||||||| || |
----gtatgcttccatgt--tttaaaacttgattgtgtgaagcagttttagccataagccttgttaatgaataagggaa--aactgatacttattttcaa--caataatgtg----actgtgatgtaatgc-agGACGGTTATGTTCCATATCACTCAGCAAGAATCGAGTCATGCCAACCTGCTTCTTTCGACAGCTCGAAAAGGGGAGTTGCCTTCTTGGAAATGCTGAATA

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv12s0055g00430.t01 (Vitis vinifera), 3'ss of exon 13
gttatcccctttccacgtgattaacagctttaatttacatgtgaatcagagttgtggctgctctgaatctttcagcatttct-----aatgatct--ttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
                                        |  | |     |||||  |||| ||  | |||  |  |||       |||| | |  ||  |  |  | |   ||||  ||  |||         |  |||||||||||||| ||||||||||| || ||||||||  | |||| ||  || ||||  ||  |||||| ||||||| |||| |||   || ||||| ||  
----------------------------------------gatagttcccattgtgcttgctttgtttttttttgttttttccctcgaatgttttgtttgctctgctaactccagttctta-tattgctactgtgtctcagGATGGTTATGTTCCATATCATTCTGCCAGAATCGAATTGTGCCAGGGAGCTTCATGGGACTACTCAAAGAAGGGCAAAGTGTTTCTGGAGATGCTGAATG

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|58597607|gb|CK008135.1|CK008135
EST:     TGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG                         GATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA
genomic: TGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAGgttatcccct ... gccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA
EST: gi|29613529|gb|CB618542.1|CB618542
EST:     AAGACACTGGAGAACTTCAAAAATATTTATACTTTCTATCTTCACCACAG                         GATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA
genomic: AAGACACTGGAGAACTTCAAAAATA-TTATAC-TTCTATCTTCACCACAGgttatcccct ... gccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA
EST: gi|33381178|gb|CF196521.1|CF196521
EST:     TGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG                         GATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA
genomic: TGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAGgttatcccct ... gccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCA

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: 46 (upstream exon), 57 (downstream exon)
Score: 15

TTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAGgttatcccct ... gccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatgatctttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA
                              ttgtaac  putative branch site (score: 15)
                                      ttttcttgcc  CT-rich tract
       atctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcccctttccacgtgattaacagctttaatttacatgtgaatcagagttgtggctgctctgaatctttcagcatttctaatgatctttatttcgaaatcatgagtttgtaacattttcttgccataccagGATGGTTATGTACCATATCATTCAGCAAGAATCGAGCTCTGCCCGGCTGCATCATCAGATAACTCAAGGAAGGGCCAAGTCTTTACAGAAATGCTCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA