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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatataggagcattccacaccatatttttatacatagatatttttatagttccttctgggatctgagcatattattcactgagctgaatcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC

Basic information

species Oryza sativa
transcript LOC_Os01g59600.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G445100_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------tgcatataggagcattccacaccatatttttatacatagatatttttatagttccttctgggatctgagcatat--tattcactgagctga--atcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
                                                                                          | | |  |||     ||| | ||||||        ||    |   |   ||| || | |   |  | ||  | || | |||  | |  | | ||||||||||||||| ||||||||  |||| || ||||| ||||||||||| ||
gtaagttgttactgtattgcatagttgtatcaatgtgagtgcataggcttatggctttagctttttcatgaattatgcatcccaccagtcacacgttcatgaatgaccttgtttttaagttgcattacacattaggagtcttgtgagtttgaaatacataatgtttattgactttacgaacttgaacagAAATACTTCGGTGCTGCATTGGGGAAGGGAAGGCAGGCTGCAAAGAC

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 7
tgcatataggagcattccacaccat-atttttatacatagatatttttatagttccttctgggatctgagcatattattcactgagctga--atcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
  ||| |        |  |  ||||  ||||||   |   |||   || |||     |   | || |||  |   || |   |||| | |  | | ||||||||||||||||||||||||  | || || || |||||||||||||||||
--cattttcagtacgtagatgccattgtttttaagtagcaatacactt-taggagtgttgtgaatttgaaaaacataatgtttgagtttacaaacttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G130398_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------tgcatataggagcattccacaccatatt-tttatacatagatattt--ttatagttccttctgggatct----gagcatattattcactgagctga--atcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
                                                                                       ||   |    || |    |    ||| ||| ||  |||   ||   ||   |   ||| ||  || |    |  |||| | || | ||   | |  | | ||| ||||||||||| ||||||||  |||| || ||||||||||||||||| ||
gtaagttgttactgtattacatagttgtatcaacgtgagtccataggctcattagttttatttgaattttgttttccatcagtcgcacactcattttcagtatggatggcattgtttttaagtagcctttcactttaggagtcttgtgaaattttgaagtacataatgtttattggcattacaaacttgaccagAAATACTTCGGTGCTGCATTGGGGAAGGGAAGACAGGCTGCAAAGAC

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G028346_T01 (Zea mays), 3'ss of exon 5
tgcatataggagcattccacaccatatttttatacatagatatttttatagttccttctgggatctgagcatat--tattcactgagctga--atcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
   || |   || ||     ||| | |||| |        |||  |    |   ||| ||   |   |  | ||  | |||| |||  | |  | | ||||||||||||||||||||||||  |||| || ||||| ||||| ||||| ||
---atgttc-agtatggatgaccttgttttcaagttgcattatgctctaggagtcttgtgaatttgaaatacataatgttcattgactttataaacttgaacagAAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC

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|88847361|gb|CI011304.1|CI011304
EST:     ATAGGGATGGGCCACAGCTCT-TATGATCGAACCCTCAGGAGTCTCATAC                         CAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|88976521|gb|CI024666.1|CI024666
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         GAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|27576784|gb|CA999478.1|CA999478
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGG
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGG
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86597380|gb|CI280517.1|CI280517
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86841716|gb|CI337401.1|CI337401
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|29668732|gb|CB665007.1|CB665007
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86836032|gb|CI346125.1|CI346125
EST:     ACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|163920473|gb|EG709578.1|EG709578
EST:     TAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: TAGGGATGGGCCACAGCTCTACATGATCGAACCCTCA-GGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|8859855|gb|AU097173.1|AU097173
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|8856768|gb|AU094086.1|AU094086
EST:     ATAGGGNTGGGCCACAGCTCTACATGANCGAACCCTCAGGNGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|33686717|gb|CF314956.1|CF314956
EST:     CATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: CATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86543850|gb|CI184056.1|CI184056
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|33692106|gb|CF320345.1|CF320345
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86890281|gb|CI321458.1|CI321458
EST:     CTCTACATGATCGAACCCTCAGGAGTCTCAAAC                         AAATACTTT-GTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: CTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86545852|gb|CI186058.1|CI186058
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|88694188|gb|CI738226.1|CI738226
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAA
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAA
EST: gi|88250600|gb|CI348830.1|CI348830
EST:     ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
EST: gi|86870489|gb|CI320585.1|CI320585
EST:     ATA-GGATGGCCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATAC                         AAATACTTTGGTGCTGCTCTGGGTAAA-GAAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC

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), 47 (downstream exon)
Score: 117

GCCTTTTGGTTGTGGAGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaac ... tcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagttccttctgggatctgagcatattattcactgagctgaatcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC
                         atattattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatataggagcattccacaccatatttttatacatagatatttttatagttccttctgggatctgagcatattattcactgagctgaatcctgaacagAAATACTTTGGTGCTGCTCTGGGTAAAGGAAGACAGGCTGCAAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA