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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatttgccctatctttgctagttagttctatgatttatctattcccactgtttggctgtcctgtcccaaaatatagca...

Basic information

species Oryza sativa
transcript LOC_Os12g07450.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G096070_T01 (Zea mays), 5'ss of exon 8
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatttgccctatctttgctagttagttctatgatttatctattcccactgtttggct----gtcctgtcccaaaatatagca--
||||||||||||| || || ||||| ||||| ||||||||||||||||| | |||||||||||||||||| ||||||||||| ||||||||| ||  |    |   | ||  |||    |   ||||  |  ||   | |     ||| | || ||  ||||  |||     || | |  | | ||||   |  
GTTATTTGAGAGTATTCGATTTTTCAAAGGAACAACTAATATTTGGTGGAAGAAGTTATTATGGTGCACTGTTGTGTTGCACTTGGAGgtaagtgtgaatggcttgtgtagttttatttt---tttgggaaatatacccaca---tatgtgtttcccttgttatgctctttatcgtctatccacatattttatg

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G20240.1 (Glycine max), 5'ss of exon 9
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccactttta------catttgccctatctttgctagttagttctatgatttatctattcccactgt---ttggctgtcctgtcccaaaatatagca--------------------------------------------------------------------------------------------
|||||||  |||| ||||| |  |  || || ||||| |||| ||||||||||||||||||||||||  | || |||||  | ||||||| |  || || |    ||||       || ||     |||||||    ||| |    |  ||  ||  ||||     |    | |||     |   | ||| ||| ||                                                                                            
GTTATTTACGAGTATTTGATTACTTAAAAGAACAACTTATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAGgtga--ggcatatttggttttggtcaatcaattaatggatctttg--gattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaa-ataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacag

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G33740.1 (Glycine max), 5'ss of exon 8
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatttgccctatctttgctagttagttctatgatttatctattcccactgtttggctgtcctgtcccaaaatatagca
|||| ||| |||||||||| |  || || |||||||| |||| ||| ||||||||||||||||||||  | || |||||  ||||||||| | |    | |     |    | ||    | |  |       |   |  || ||||  ||||| ||   |||   || |        |   ||||  |
GTTACTTGCGAGTGTTTGATTACTCAAAAGAGCAACTTATATGTGGCGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCATGGAGgttagtcttgtttggttctagttaattaatttgtgatattggaatttatagatcattttcctatttccctagttcaccttttactctagagcttatataa

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G05890.1 (Glycine max), 5'ss of exon 9
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatttgccctatctttgctagttagttct--atgatttatctattcccactgtttggctgtcctgtcccaaaatatagca
|||||||  |||||||||| |  |  || || ||||| |||| ||||||||||||||||||||||||  | || |||||  | ||||||| |  || || |    |||||  |   ||   |  | | | |  |  | |  || | |   ||||| || | |||      |        |   || ||| 
GTTATTTACGAGTGTTTGATTACTTAAAAGAACAACTTATATGTGGTGGGAAAAGTTATTATGGTGCTTTGTTATGTTGTGCTTGGAGgtga--ggcatatttggttttaagtcaaccaattaatggattgccatctttcgattaatctcctatttcctcagttcattcctttcactagactctagagct

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G37160.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctcca--cttttacatttgccctatctttgctagttagttctatgatttatctattcccactgtttggctgtcctgtcccaaaata----tagca-------------------------------------------------
||||| |  || | ||||| ||||| |   |  | ||| | | |||||  ||||||||||||||||| |||||||||||  | ||||||||| |||| |||  |  |||| |||  ||    |||||  ||| ||   | | |     |   ||   |  ||||    | | ||  | |||  |     |||||                                                 
GTTATCTTCGAATTTTTGATTTTTCAACCCAAAAGCTAGTGTGTGGTGTAAAAAGTTATTATGGTGCTCTATTGTGTTGTGCTTGGAGgtaactgga-tctaaatcctttgacaaatg----atcttcccta-ttgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgctaacattgcgattggcctgacag

upper sequence: LOC_Os12g07450.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 5'ss of exon 8
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatt---tgccctatctttgctagttagttctatgatttatctattcccactgtttggctgtcctgtcccaaaatatagca
||||| |||||||||||||||| || |  || ||||| |||| |||||| ||||| ||||||||||| ||||| |||||  | ||||||| |      |  ||| |||| ||||   |  |  ||| ||  |  | |    | |   || | | ||       |||     |  | |    | |||||   
GTTATCTGAGAGTGTTTGACTTCTCAAGAGAACAACTTATATGTGGTGGCAAAAGCTATTATGGTGCTCTATTATGTTGTGCTTGGAGgtgaccaactttaccagtttt-cattgcataacagatcattttttttcaaaattgtttctttttttttaatggattttttaaattatatatatatatatat--

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|29670875|gb|CB667150.1|CB667150
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|29665681|gb|CB661956.1|CB661956
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|4715313|gb|AU056430.1|AU056430
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|4715180|gb|AU056297.1|AU056297
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|218478110|gb|FG955323.1|FG955323
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|33822326|gb|CF336974.1|CF336974
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
EST: gi|58685449|gb|CK074136.1|CK074136
EST:     ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAG                         CTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT
genomic: ATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGT

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), 66 (downstream exon)
Score: 31

GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaa ... gtttttacagCTCGGATGGCAAATATCTGTTGACTGGTGGTGAAGATGATCTTGTGCAGGTATGGAGCATGGATGACAGAAAGATAGTCGCGTGGGGCGAAGGGCATAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTTGAGAGTGTTTGACTTTTCGAAGGAGCAACTAATATTTGGTGGGAAAAGTTATTATGGTGCACTATTGTGTTGCACATGGAGgtaattggaatctccacttttacatttgccctatctttgctagttagttctatgatttatctattcccactgtttggctgtcctgtcccaaaatatagca

- - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtccc