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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagtgcttttttcactagtattcgtatcttcttgtttatgcttagtatacacacgctgtaataactgcttttttgttgtcttatggaaccactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 26
gcagtgcttttttcactagtattcgtatcttcttgtttatgcttagtat-acacacgctgtaataactgcttttttgttgtcttatggaac-cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG
  | |  ||||   ||     ||| | | |   ||| ||||    | || ||  |   |    |  |  |      |   |  | |   |  |  | || ||| ||||| || || ||||||||||||||| ||||||| |||||||||||||||||||||||||| || || || || |
--acttgttttcatacccaccttcctttatatctgtatatgtactgcatgactgaaatttgtttctcaacacaagagggattatttacgatgctttctgcagACCATTACGACGTGAAAATGCCTTGCCATTTGATTCTATCAAAGCTAGCAGACAAGTGCCCTTCCGCCGTCCTTGCTG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 26
gcagtgcttt-tttcactagtatt-cgtatcttcttgtttatgcttagtatacacacgctgtaata--actgcttttttgttgtcttatggaaccactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG
  | | |||| ||| ||| ||| | |  |     |||   || |||| | | |     || || |   |||  ||||  |    || || |      |||| ||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| |||||||| |||||||| ||  ||||||
-gaatactttattttactggtaatgctcaagggattgaggat-cttatttttctgtttctttattggtactaattttaaggatactcattgtgtt--tttgcagATCATTATGATGTTAAAATGCCATGCCACCTGATACTCTCGAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 27
-----gcagtgcttttttcactagtattcgtatcttcttgtttatgcttagtatac-acacgctgtaataactgcttttttgttgtcttatggaaccactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG
      |||| |     |  |  ||  | ||| | |   | ||   |||  | | | | |  |  | |  |||  ||||  |    || || |      |||  ||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| |||||||| |||||||| ||  ||||||
tagacacagtac----atagcaggtgcttgtagcattaggctttccctttcttttctaaattcgttgaatactaattttaaggatactcattgtgtt--ttttcagATCATTATGATGTTAAAATGCCATGCCACCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 26
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 27
-------------------------------------------------------------------------------gcagtgcttt--tttcactagtattcgtatcttcttgtttatgcttagtatacacacgctgtaataactgcttttttgttgtcttatggaacca---ctttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG
                                                                                |  |  |||  ||||| |     |  ||     |  || ||| ||  |||||      | || |   |   ||  ||   |   || ||       |||   ||||||||||||||| ||||||||||||||||| || || ||||| || |||||||||||||| || || ||  ||||||
gtgcgtttttatttttttatttttaacaagaccatcattcttttttacttcactttatttttttcacccttttccccccactttagtttagtttcatttcagctgctaaaagttatttcatgtttc-tatacttgaagtttagtttatcacttcctgaactgaaattgatttggctcttctcagATCATTATGATGTCAAAATGCCTTGCCATCTTATCCTTTCAAAACTTGCAGACAAGTGCCCATCCGCCGTATTGGCAG

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|58654892|gb|CK043572.1|CK043572
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTAAGGTG                         ATCATTATGATGTAGAAATGCCTTGCCATCTGATTCTCTCAAAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAG
EST: gi|58672731|gb|CK061417.1|CK061417
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|2798908|gb|AA752202.1|AA752202
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|86478996|gb|CI121629.1|CI121629
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|38473429|gb|CF957561.1|CF957561
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|66914920|gb|CX101768.1|CX101768
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|163919951|gb|EG711701.1|EG711701
EST:     CGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: CGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|32948231|gb|BP184803.1|BP184803
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|58603061|gb|CK013589.1|CK013589
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCGAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|58667112|gb|CK055798.1|CK055798
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAG
EST: gi|29625622|gb|CB630633.1|CB630633
EST:     AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTG                         ATCATTATGATGTAAAAATGCCCTGCCCATCTGATTCTCTC
genomic: AGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCC-ATCTGATTCTCTC

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), 75 (downstream exon)
Score: 34

AAAGCTGCCTTTGAATGTGTGGATACATTGCTGGATAGCTGTCTTGATCAAGTGAACCCATCATCATTTATCGTTCCTTTCCTCTTATCTGGTTTAGGTGgtaagtactg ... cactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatacacacgctgtaataactgcttttttgttgtcttatggaaccactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG
              taataac  putative branch site (score: 34)
                                            ccacttt  putative PPT
                        ttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagtgcttttttcactagtattcgtatcttcttgtttatgcttagtatacacacgctgtaataactgcttttttgttgtcttatggaaccactttgtagATCATTATGATGTAAAAATGCCTTGCCATCTGATTCTCTCAAAGCTAGCAGACAAGTGCCCTTCTGCTGTTCTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - tgctttt
- - - - - - - - - - - - - - cttcttg
- - - - - - - - - - - - - - - - - - -tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - cacacgc