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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 7
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag
|| |||| |||||||| || || || |||||||||||| | || |||||||||||||| |||  |||||| ||||| ||||| ||||||||| ||||||||||||| | |   || || |||||| ||| ||  |  | || ||  |  || || ||  |  | |        ||        ||||||
AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatcttgacagcaatatgtgataaacttcgatatcttattgaactcagttaccagtattaaccgtgccaaatggtcatgattcag

upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA09G30910.1 (Glycine max), 5'ss of exon 7
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgttt----gatacaa--tttccgatgctgataaaaatcaactacttcaa-----ttcag------------------------------------
 ||| || ||  |  | ||||||  ||||||||| ||||| || |  ||||  |  ||| |    ||||||||||||||||||||||| ||| |||| |||||| |   |     || ||| ||  ||   | | | |  | | |      |||||   ||  | |    ||   |||   |  || |||     ||||                                     
GGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAGACTTTCATATTGGATGgtaaaaatctt----tagcatttgttaa--ctgaggatcctatattgcaagtacaagtctttagttatgaatgtgaattttcccctgcaaagactttcacacgcttgataacaataataatgcttaaattcaccag

upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G11310.1 (Glycine max), 5'ss of exon 7
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaaga--ccatagaagtaacatgtgacaaagt--taaaggttttgtttg-atacaat-ttccgatgctgataaa-aatcaactacttcaattcag----
 ||| || ||  |  | ||||||  ||||||||| ||||| || |  ||||  |  ||| |   |||||||||||||||||||||||| |||||||| ||||||    |  ||  | |    | | | ||| |  || | |   ||  || | |||   ||   |  ||   ||  |||||   |   ||||  |     
GGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAGACTTTCATGTTGGATGgtaaacatctttaacatttgtttttaagaaaatagtatatgcactgactgtacacaggatttttacactttcaaccaatcacaaatcacaatatatgata

upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT3G18070.2 (Arabidopsis thaliana), 5'ss of exon 4
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag--
 | | || ||  | || ||||||  ||||| ||| || || || |        | |||| | |  || ||||||||||| ||||||||||||||||| ||||||      | |  |      | | |   ||  || |    |||| |  |  ||   |   |        |       |    ||     
GGGTTGGGATTCTACTGGATTTTGTTTGGTTTGAGCCACTTACGAGTAGTCAAGCAGACAATGACGCTGCTCAAAGAGCAAGAGACTTCCATGTTGGATGgtaacggttcaaacttttggactcatatttttccagttacattttggtg-agcttataagaatatcttttgtgtggggataatgtttgaag

upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 5'ss of exon 7
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag-----
 ||| |||||  |  | ||||||  ||||||||| ||||| || |  ||||  |  ||| |   ||||||||||||| |||||||||| |||||||| |||||  |  |      |  |||    ||  | |  ||  |  | |  || || | |  |||  | | | |       |  ||   ||        
GGATTGGAATTCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAACCTAGCAGCTCAAAGATCCAGAGACTTTCATGTTGGATGgtataaatact----tggcattctccactgattcagagtaggatgaatgcagtata-gatattcaaatagtaatgttggttttgttttctatag

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|58657560|gb|CK046240.1|CK046240
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58658600|gb|CK047280.1|CK047280
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58669788|gb|CK058474.1|CK058474
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58596985|gb|CK007513.1|CK007513
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58604470|gb|CK014998.1|CK014998
EST:     CTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: CTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58668081|gb|CK056767.1|CK056767
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58671028|gb|CK059714.1|CK059714
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58664913|gb|CK053599.1|CK053599
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGC
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGC
EST: gi|33684008|gb|CF312247.1|CF312247
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATAT
EST: gi|58612072|gb|CK039784.1|CK039784
EST:     ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTG                         GTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGA
genomic: ACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGA

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: 75 (upstream exon), 64 (downstream exon)
Score: 22

AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccat ... ttcaattcagGTTTCTTGATCCGTTAATAAATGGACAATATCCAAAAAATATGCGAGATATTGTGAAAGAAAGATTACCTACTTTCACGCCTGAACAAGCTAAGCTAGTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA