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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgttatcttcttcagaaacttttccatctggctatgcatatcatacttggctgtgtacgtgtag

Basic information

species Oryza sativa
transcript LOC_Os12g02390.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 7
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgtta----tcttcttcagaaactt-----------------ttccatctggct-atgcatatcatacttggctg-tgtacgtgtag
|||||||||||||||||||| | |||||||||||||||||||||||||| ||||||||||||||| |||||||||||||||||  | ||||||||    | ||||| ||||| |                  ||| ||    || || ||||| |||||||  || | ||  |  ||
ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAGgtatttgctgtggtgttagtttttttcttgagaaattggttttgtcaaatatttgttctattcaacttatacatataatacttgtttggtttatatacag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgttatcttcttcagaaact----tttccatctggcta-tgcatatcatacttggctgtgtacgtgtag----------------------
||||||||||||| |||||| | |||||||||||||||||||||||||| |||||||| |||||| |||||||||||||| ||| | ||||| | | || ||   |   |    |||   | |  | | |   | |  |  || ||| | | | ||||                       
ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagct-tatgcatgtaatgtgttttcggtttatatacag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G00510.1 (Glycine max), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtattt--cttatggt--gttatcttcttcagaaacttttccatc-tggctatgcatatcatacttggctgtgtacgtgtag-------------------
| ||  ||||||||||||| ||| | ||||||||||| |||||||| ||||| ||| |||||||  ||||||||| |||||||   | || ||  |  || || ||  ||||  ||| |||       || ||| |       |||| |    || |                     
ACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGGgtatttggttaattgtcagccatatttttgtgaaatgtttacattactataatacatgtggggtcaggctcttatggtttcaattgttttcctaatcatag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G41070.3 (Glycine max), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgttatcttcttcagaaacttttccatctggc-tatgcatatcatacttggctgtgtacgtgtag-------------------------------------------
|  |  ||||||||||||| ||||| ||||||||||| |||||||| |||||  || |||||||  ||||||||| ||||||| |  |    | | | |  ||||  || ||    |      | |   | |     |  | || |  |  ||                                             
ACCTGGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGGgtattt-tggttaactgaaccttgtcaggcacattattgtgaaaagtgtatgttttcacttcagatgggatctggttcttccggttttaaccgtatacatattttatatttctaactatag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G14800.1 (Glycine max), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttctt-------atggtgttatc----ttcttcagaaacttttccatc-tggctatgcatatcatacttggctgtgtacgtgtag-----------------
| ||  ||||||||||||||||| | ||||||||||| |||||||| ||||| |||||||||||  ||||||||| |||||||  |       || |||| | |    || ||  ||||  |||  ||       || |||     |   |||| |    ||  |                  
ACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGGgtatttagttaactcaatcgtgtcagccatatttttgtgaaatgtttatattactataatacatgcgggatcaggctcttctggttaattgttttcccaattatag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G44580.1 (Glycine max), 5'ss of exon 6
-ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgttatcttcttcagaaacttttccatctggctatgcatatcatacttggctgtgtacgtgtag----------------------------------------------------
 |  |  ||||||||||||| ||||| ||||||||||| |||||||| |||||  || |||||||  ||||||||| |||||||  |    ||  | | |  ||||  || ||   ||   |  | |  ||| ||  ||  || |  |  ||                                                       
GACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGggtatttggttaactg--aaccttgtcaggcacatt---attgtgaaaagtttattatgtttt-ctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataaca

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatg-gtgttatcttcttcagaaact---tttccatctggctatgcatatcatacttggctgtgtacgtgtag------------------
|| |  |||| ||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||  ||||||||| |||||   ||  |  || |||  | ||||    ||   |||   | | | | |   ||  ||   ||  |       | | |                  
ATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGGgtatcatttgggcatgctattcttttcattttctaacttttggttttgttgttgctactatgactgattactcttatttggtatgaatcggcattttag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 6
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtattt------cttatggtgttatcttcttcagaaacttttccat---ctggctatgcatatcatacttggctgtgtacgtgtag-------------------------
|  || | ||||||||||| ||||| || |||||||| || ||||| || ||||||||||| ||  |||||||||||||| ||      ||| ||    | || | ||  |     | | |||    | | |  | ||   ||  ||  ||||    ||||                           
AGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAGgtacttttatgtcttttgcctgtttcctgttatgcgttctctgcatgtcttcgtttgggattcaatggttctctgttatggtgttcttctgatcaaataattttgttatag

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|569920|gb|D40769.1|D40769
EST:     ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG                         GACACTTTTCGTGGGAGAGTTTGTGAAT
genomic: ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttctta ... gtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAAT
EST: gi|570122|gb|D40971.1|D40971
EST:     ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG                         GACACTTTTCGTGG
genomic: ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttctta ... gtacgtgtagGACACTTTTCGTGG
EST: gi|571715|gb|D41226.1|D41226
EST:     ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG                         GACACTTTTCGTGGGAAGAGTTTGTGAATGTCCAGTTGTAAAAGGTGTTAA
genomic: ACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttctta ... gtacgtgtagGACACTTTTCGTGG-AAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAA

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: 57 (upstream exon), 53 (downstream exon)
Score: 14

ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttctta ... gtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAGgtatttcttatggtgttatcttcttcagaaacttttccatctggctatgcatatcatacttggctgtgtacgtgtag

- - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT