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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagataactctcgtccttgtcattattagtacgggtacttgctgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA

Basic information

species Oryza sativa
transcript LOC_Os10g31000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
-----------------gtgagataactctcgtccttgt-cattattagtacg-ggtacttgctgtttattctagcttctataaccctgggttgaatatt---tccatg---aatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
                  |   || | |    ||   |  | ||||  |||     |    |||   | || |    ||| | |     || | ||  ||    | |||    || ||| |||||||| || ||||||||||| |||||||||||||||||||| || || || ||||||||||| |||||||||||||| || |||||  |||||||||||||
gtaagattgatctttacatctcattattaggatctccgcgccttatctgtatacaattagcgctccatgttttgtactctgttataacagggttaactttgaacctatgtgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
------------------------------------------gtgagataactctcgtccttgtcattattagtacgggtacttgctgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
                                          ||    |  ||||   |||| ||  ||    ||  | | | || | | || ||| | |   | |    |   |||||  | |   ||| | ||| |||||||| |||||||||||||| |||||||||||||||||||| || || || ||||||||||| |||||||||||||| || |||||  |||||||||||||
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgtactct-gttataacagggttaacttgaacctgtgtgtga-tattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
---------------------gtgagataactctcgtccttgtcattattagtacgggtacttgctgtttattctagcttcta--taaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
                      |   || ||   | | |||| |||    | |      |       ||| ||   ||  |||  |||   | | |     | ||   ||| ||  |  |||| || ||||||||||| || || || ||||| ||||||||  ||||||| ||| | || || ||||||||||| || ||||||||  ||||||| || ||
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------gtgagataactctc--gtccttgtcattattagtacgggtacttgctgtttattctagcttctataaccctgggttga-atatttccatg--aatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
                                      |    |||||     ||| |  || || |    |  | | ||| ||  || |   || |             ||||| || ||||  |   | || ||  ||||| | || |||||||| ||||| || ||||| ||||||||  | ||||| || || || || ||||| |||||||||||||| || ||||||||||| ||
gtaagataatgtcctacaatatttctttttccgtggcttctactaacttcaaagtcatgttccttttgctcatagattcttccttgttttatcagttgtctgcttaagaagttgatatctttcttttttatttattaacagATTTGGTAAATGTGTTTGAAGTGTTTCTTCCTCAACTTCTTCTCTACCCCAACCCATCAGATCCATTGAATGGAGAGGCTGCAGCCCTGATGATGCGAGA

upper sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gtgagataactc--tcgtccttgtc-attattagtacgggtacttgctgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
                                         |  ||   |    ||||   | |  |  |  |  |  | |||||  |  || |  | | ||     ||  |   | | || ||  ||    | |||  ||||||| || || ||||| || || |||||||| |||||||| ||||| || || || || || |||||||||||||||||||| || || |||||||||||
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgtta-tcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA

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|163920118|gb|EG709876.1|EG709876
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|33654410|gb|CF277024.1|CF277024
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|58659537|gb|CK048217.1|CK048217
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|38478467|gb|CF962600.1|CF962600
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTGAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|27410240|gb|CA923310.1|CA923310
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGT
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGT
EST: gi|163927163|gb|EG715184.1|EG715184
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|86896481|gb|CI328868.1|CI328868
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|58681245|gb|CK069932.1|CK069932
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|86854335|gb|CI254280.1|CI254280
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCGTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
EST: gi|218478509|gb|FG954791.1|FG954791
EST:     TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG                         ATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA
genomic: TGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAA

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: 53 (upstream exon), 75 (downstream exon)
Score: 101

GTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTGgtgagataac ... tttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA
               ctataac  putative branch site (score: 101)
                                             ttttt  putative PPT
                            ttgaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagataactctcgtccttgtcattattagtacgggtacttgctgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC