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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC

Basic information

species Oryza sativa
transcript LOC_Os07g47100.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 7
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
     | || ||||    ||  | ||   ||  | |    |  | |    ||  || |  ||         | || ||  |  |  || | | ||||| | ||||| || ||||| ||| |||||||||| ||||||||||||||||||||||||||||||||||||||  | || || || || ||||||||||||||||||
----gtaattattccttgtcattttttcgctagtaatgtttctgttctgcttaataaacgaatgctgactgaattccttttgggcctttttcattcac-ttagGCATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGAC

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 8
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
                |    | ||||| |     | | || ||           |     |||||  | |   ||||    || ||  |       |  |||||| |  ||||| ||| |||| ||||||||||| |  ||| ||||||| ||||| |||||||||||||| ||||| ||||| |||    |||  ||| | 
--------------gtacgtgaaattcttcaacacattcatgagacatgtacaagattgctactaatgata--ctacttaactgattaatttccctgctgcagGCATGTTTTTGCCACTTTGTCATTCATTGCTGAAATCTTTATCTTCCTCTATGTGGGGATGGATGCATTAGATATAGAAAAGTGGCGAATTGTAAGTCAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 9
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaacta--aacaaaacttactggtttgttttgtcctttc-acctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
                |    | ||||| |     | | |||||      |    |  | | |||  ||  | |||   |   |  ||||    |  |  || |||||| |  ||||| ||| |||| ||||||||||| |  ||| ||||||| ||||| |||||||||||||| ||||| ||||| |||    |||  ||| | 
--------------gtacgtgaaattcttcaacacattcattaggc---atgtacaagatagctactaatgatactacttaactgattttaatttccctgccgcagGCATGTTTTTGCCACTTTGTCATTCATTGCTGAAATCTTTATCTTCCTCTATGTGGGGATGGATGCATTAGATATAGAAAAGTGGCGAATTGTAAGTCAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 10
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
           |     ||| | ||     |  | ||    ||    || |    |   |  |||  || | | ||    | | |||  |||        ||||||  | ||||||||  |||| ||  |||||||||  ||| ||||||| |||||||| |||||||| ||||| |||||||||||| | |||| |||||| 
----------gtatgtcttctaaatagatttcctcaagatatacgcacactgtcca---agtctatgcata-cctaaacatatttttcatccaactcttgcagGCATTCTTTTGCAACCTTGTCTTTTGTTGCTGAGATCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAATGGAAATTTGTCAGTGAT

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 10
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
|||  |     |||| |    || | ||   |||   |     |    |||   | | | | ||||||| |             |||   ||        ||||||  | ||||||||  |||| ||  |||||||||  ||| ||||||| |||||||| |||||||| ||||| |||||||||||| | || | |||||| 
gtatgtc----ttctaaacagatttcctcaagttatgtacactgtccaagtctat-gcatacctaaacatat------------tttcacccaactcttgcagGCATTCTTTTGCAACCTTGTCATTTGTTGCTGAGATCTTTATCTTCCTTTATGTTGGTATGGATGCCTTGGACATTGAAAAATGGAAATTCGTCAGTGAT

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacct---cagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
        ||||      ||||| ||||     || |  |  |  |  | |   |   |    |   ||| |||||||   ||  | ||   || |       |||||| || ||||| ||| |||| ||  | |||||||||||| | ||||| || ||||| |||||||||||||| || || ||||||   || |  ||||||
-------gtaatatgacctccattttct----cttgaaaacaaattcaaatgttttcca----tcttcaatacttacttactttctatgcatttacgatgagacagGCATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGAC

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 9
---------------gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctt--tcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
                 ||||  |   ||  | ||   |  | | | | | || |||   ||   | |  | ||||| ||      |  || |   |  || |||   |  |     ||||||  | ||||||||  | || ||  || |||||| |||| |||||||||||||||| || ||||| ||||| ||||| || |||  | |||  ||  ||
gtaagctaaatcttcagaaatattttctcaaaatctggaacccattttcttattattttattttttcccaaaaaaaattatgttgcatgtattttctgtttctgtttatgatttttgcagGCATACTTTTGCAACGTTATCTTTTGTTTCTGAGATTTTTATCTTCCTGTATGTTGGTATTGATGCCTTGGACATTGAGAAGTGGCGGGTTGTAAGCAAC

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|88577662|gb|CI674260.1|CI674260
EST:     TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAA                         GCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
genomic: TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
EST: gi|27549114|gb|CA767092.2|CA767092
EST:     TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAA                         GCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
genomic: TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA

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), 72 (downstream exon)
Score: 18

TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC
                      aacttac  putative branch site (score: 18)
                                tttgttttgtcctttc  putative PPT
         aaaaactaaacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA