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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttctcagattaccgtaatttaatatatgcatgtattatattacatcgtgctagtgtgataaacatttgtgatccattcaatcaatcattgtattatgatagttgaatttgacctcattgcttgatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCATGTGATGGTCTCCTCATCTACGCCGGATTTTGTGATGGTGCAATTGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g06480.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 23
gttagttctcagattaccgtaatttaatatatgcatgtattatattacatcgtgctagtgtgataaacatttgtgatccattcaatcaatcattgtattatgatagttgaatttgacctcattgcttgatca----tgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCATGTGATGGTCTCCTCATCTACGCCGGATTTTGTGATGGTGCAATTGGAG
                                  |  |||  |  |||| | ||  |   |    ||  ||| |  ||  |||| |  |   |  | || ||| | || ||| | || | ||| | | ||||    |||||||||| || | |||  |||| || ||||| |||||||||||||||||||| |||||  || | ||  | || || || ||| ||||||||||  ||||||
----------------------------------agatatggt-ctaca-catgaca-catagataatgtttcttctcttttcattgga--gtccttttttga-acttcaatcttac-tgatttcctaatcaatgttgcagTGGTCTCCGAAAGACTCACTTCCAGCTCCCATTTCAAGTGCAATATACTCCTGTGACAGTATGCTGGTTTATGCTGGTTTTGGTGATGGTGCTGTTGGAG
















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|58683930|gb|CK072617.1|CK072617
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|58683700|gb|CK072387.1|CK072387
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|33793091|gb|CF322427.1|CF322427
EST:     TGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACCT
genomic: TGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGC-TCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATAC-T
EST: gi|8956406|gb|BE230209.1|BE230209
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|33801489|gb|CF326617.1|CF326617
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|58687154|gb|CK075841.1|CK075841
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|58667666|gb|CK056352.1|CK056352
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCC
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCC
EST: gi|58588776|gb|CF987084.1|CF987084
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|27577716|gb|CB000411.1|CB000411
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|58608562|gb|CK036595.1|CK036595
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGC
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGC
EST: gi|33666456|gb|CF297423.1|CF297423
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|8956186|gb|BE229990.1|BE229990
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
EST: gi|8956739|gb|BE230542.1|BE230542
EST:     ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCG                         TGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA
genomic: ATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCA

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: 72 (upstream exon), 73 (downstream exon)
Score: 69

TGATACAAGGGTGCAGTTTCACAATGACCAAACACATATTTTGGTGGTTCATGAGAGCCAGTTGGCGATCTATGATGCAAAGCTAGAGTGCTTGCGCTCGgttagttctc ... gatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCATGTGATGGTCTCCTCATCTACGCCGGATTTTGTGATGGTGCAATTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcaatcattgtattatgatagttgaatttgacctcattgcttgatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCATGTGATGGTCTCCTCATCTACGCCGGATTTTGTGATGGTGCAATTGGAG
     aatcattgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttctcagattaccgtaatttaatatatgcatgtattatattacatcgtgctagtgtgataaacatttgtgatccattcaatcaatcattgtattatgatagttgaatttgacctcattgcttgatcatgcagTGGTCCCCAAGAGAAGCACTCCCTGCTCCAATTTCAAGTGCAATATACTCATGTGATGGTCTCCTCATCTACGCCGGATTTTGTGATGGTGCAATTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG