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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgcagttctgtttggctggcataaactgtagtaagctctcttgagatgaaataagccagttctattgacaatattttccatggttatggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC

Basic information

species Oryza sativa
transcript LOC_Os07g08790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC148167.6_FGT001 (Zea mays), 3'ss of exon 2
---------------------------------------------------------tgactgcagttctgtttggctggcataaactgta----gtaagctctcttgagatgaaataagccagttctattgacaatattttccatggttatggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC---
                                                         |   ||    || |   | ||   ||   |  ||    |  |    | | || ||||||  || ||  | || |||||| |||||  |  ||   |  ||||||||||||||| | ||||||||||||||||| ||| ||||||  ||||| || ||||| || ||||| |||||||| || |||||   
gtctggtagtcatctgtaccctcctttgaactgtaccctttaggcctcatgtacttctctttgtttctcagacagtcttctatttgccttacgctgccaaacttttggacatgaaactaggcaactttaatgacaa-attttgtactgtgtggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC

upper sequence: LOC_Os07g08790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G082809_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------tgactgcagttctgttt---ggctggcataaactgtagtaagctctcttgag-atgaaataagccagttctattgacaatattttccatggttatggatt-gcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC---
                                                             || ||    | | || |      || | ||  |||    |    || ||||  ||||||  || ||  | || ||||||  | | |  |  || |||||| ||||||||||||||| |||  |||||||||||| ||| |||||| |||||| || ||||| ||||| || |||||||| || |||||   
gtctggtagtcatttgtacgctcctttcaactgtgccctttgggcttcatctacttctctttgtctctcataccgtcttctatttgccttacgctgccaaattaacttttgaacatgaaagcaggcaactttagtgacaaactatactgt--ttgtggatttgcagAGTCCATCAGTCACATGCAGGAAGCCTCTCCAATCTGACAATACTTCTCACAGTCAAGAAGAGGACTCATATTCTGTCACTTCTTC
















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|29668088|gb|CB664363.1|CB664363
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
EST: gi|58602031|gb|CK012559.1|CK012559
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGACGCCTCTGCAAGCTGACAGTACTTCCCAT
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
EST: gi|58684078|gb|CK072765.1|CK072765
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
EST: gi|66925010|gb|CX111858.1|CX111858
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTAC
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTAC
EST: gi|29668090|gb|CB664365.1|CB664365
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT
EST: gi|58669084|gb|CK057770.1|CK057770
EST:     AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAG                         AGTCCATCAGTGACACCCAGGAAGCCTCTGCGAGCTGACAGTACTTCCCAT
genomic: AAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCAT

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: 74 (upstream exon), 50 (downstream exon)
Score: 20

TTCTGGAGAAGGAGATTGTACTCCAGTGCCTCATCCCACCAGCAACGGTGAAAAACTCTCTGATAAAAGTAGCACCTCGCTGGCAAGTATGGCGAAGAAGgtctgacata ... tggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatgaaataagccagttctattgacaatattttccatggttatggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC
                     tattgac  putative branch site (score: 20)
                     tattgacaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgcagttctgtttggctggcataaactgtagtaagctctcttgagatgaaataagccagttctattgacaatattttccatggttatggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-gactgca
- - - - - -ctgtttg
- - - - - - - - - gctggca
- - - - - - - - - - - - - - - - - - - - - - - - - -gaaataa