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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaataaaataaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtacttgtgttacataggacaactcagaa...

Basic information

species Oryza sativa
transcript LOC_Os08g08840.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G180720_T02 (Zea mays), 5'ss of exon 4
TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaataaaataaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtac--ttgtgttacataggacaactcagaa------
| |||||||| || ||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| ||| ||  |||       ||  |  | |||| |||    | |||  |  |  | | |   | |    | |  |    |  |     |||  || |        
TGGTCATACTGACTCCATTTGCTATAGCTATGGAAGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaagaatttaa------tatt-tacagttttccttgcatagttgtcaagt-atggtctccactcacattcgatgagatggctcgaaacacttcgggcatgttt

upper sequence: LOC_Os08g08840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G431314_T01 (Zea mays), 5'ss of exon 4
TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaataaaataaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtacttgtgttacataggacaactcagaa----------------------
| |||||||| || ||||| ||||| |||||||| || ||||| ||||||||||||||||||||||||||| |||| |||||||| |||||||||||||||||| ||| ||             |  |  | |||| |||    | |||| |  |        || || |   ||     ||||||  ||   ||   ||                      
TGGTCATACTGACTCCATTTGCTATAGCTATGGAAGGTCCTCAGATGTGGGCTGCTGGTTGGCAAAAGGCTGTTGCAGAAGTTGGACCCAATGTTGTCTGgtaaacaagaa-------------ttttacagttttccttgcatagttgccaagt--------gtggtctc-cacccacattacatgagatggcttgaaacactcttcatgtttttttttat

upper sequence: LOC_Os08g08840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G25290.1 (Glycine max), 5'ss of exon 4
TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaag--caataaaataaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtacttgtgttacataggacaactcagaa
|||  || |||||||| ||||| || ||| |||| || || ||||||||||||||||| |||||||  ||  |  |  || |||| ||| |  |  | ||||||   ||| || || |   |       ||||   |   | ||   ||  |||| | |||  |     | || | | ||  ||| |   || | |    ||
TTGCTATTCTCACACCCTTCGCAATTGCTGTGGAAGGACCGCAAATGTGGGCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaagaagattacttactgtaattttatcatggttacactcatctctatct-gtatgcatctctattttccatgcttta-aggtgatatcaggaaa

upper sequence: LOC_Os08g08840.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 5'ss of exon 3
TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaataaaa--taaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtacttgtgtta-cataggacaactcagaa---------------------------------------------------------------
|||| || ||||| |||||  |||| ||  |||| || ||||||||||||||||||||||||||||| ||  || |  |||| || || ||  |||||||||| |   |||||   ||| |||  ||| || | | ||| || ||   ||  ||   |  | | |  |    | |   ||  ||   |||       | ||                                                                 
TTGTGATCCTCACTCCATTTTCTATTGCCGTGGAAGGTCCTCAAATGTGGGCTGCTGGTTGGCAAAATGCGGTTTCTCAAGTCGGACCAAACTTTGTCTGgtatgatctaaaaaccaaatcaataatctttaattgtttgttaagt--tttatagactccaactcaaatgactatgagtggattggtatatattgctttagttcccttctaacttaagatataagattctaacttaatgtgttgtttttgttttttgaatcaatag

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|86498017|gb|CI140650.1|CI140650
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|88844498|gb|CI020345.1|CI020345
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|2799547|gb|AA752536.1|AA752536
EST:     GCTGCTGGTTGGCAAA-GGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|89167940|gb|CI109144.1|CI109144
EST:     NCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         TTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|86253198|gb|CI058123.1|CI058123
EST:     NCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|58590139|gb|CF988447.1|CF988447
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|87024623|gb|CI259338.1|CI259338
EST:     TCTGCTGGTTGCCAAAAGGCTCTTGCGGAAGTTGGTTCCAATGTTGTCTG                         GTGGGTTTCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|86500797|gb|CI143430.1|CI143430
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|88840622|gb|CI080076.1|CI080076
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|88842335|gb|CI081591.1|CI081591
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|58670578|gb|CK059264.1|CK059264
EST:     GGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|88837113|gb|CI078473.1|CI078473
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
EST: gi|86493864|gb|CI136497.1|CI136497
EST:     GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTG                         GTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA
genomic: GCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTA

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: 73 (upstream exon), 73 (downstream exon)
Score: 64

TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaata ... aatattgtagGTGGGTTGCTGCACAGAGCGTTTTCTACCACTTATACAACCAGGTGTCTTACATGTCTCTGGATGAGATTTCTCCATTGACATTTAGCATTGGCAATACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCATACTCACACCATTCGCTATCGCTATGGAGGGCCCTCAAATGTGGGCTGCTGGTTGGCAAAAGGCTCTTGCGGAAGTTGGTCCCAATGTTGTCTGgtaagcaataaaataaaccaagcatcctttaatttttcttcagcaattgctattttgtagcccgtagttttgtacttgtgttacataggacaactcagaa

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa