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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggtagtagcataattttgatatgctattgctcacttgtgctgctatactcacag

Basic information

species Oryza sativa
transcript LOC_Os04g55650.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G35720.1 (Glycine max), 5'ss of exon 2
-GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggtagt-agca-taattttgatatgctattgctcacttgtgctgctatactcacag------
  ||||||||||||||||| ||||| ||||||||||| || || ||  | || || || ||||| |||   ||    || |   | || |||  | | |||||   |  | |  || | | |   ||| |  ||   ||||| | || | |  ||  |||  |  |  |   |||| | | |||  |   |       
TTATGGACTATGCATTTGAGTTCATAATCAACAATGGCGGCATTGATTCTGATGAGGATTACCCATACCGTGGTGTTGATGGTAGATGCGACACATATAGggtcagtcacttggtcct-gattatttgatgattatagtagttatcactcaagttcttatattgattattttttgttcggttattttgctattgtgca

upper sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G04400.1 (Glycine max), 5'ss of exon 2
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggt------agtagcataattttgatatgctattgctcacttgtgctgctatactcacag
  |||||||||| ||||| ||||| |||||||||||||| || ||||| || || || ||||| |   ||||    || |     |||||   | ||| |||   |||   |||   | ||    |   ||   |  |      | |||| | ||| | |||   |||     | ||         ||   | ||
TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatac-ttataatagattttattcttcttatctatag

upper sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G09440.1 (Glycine max), 5'ss of exon 2
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatct---ttcgtcttctttgctcccttggtttttcaggtagtagcataattttgatatgctattgctcacttgtgctgctatactcacag-----------------
 ||||||||||||||||| ||||| ||||||||||| || || ||  | || || || |||||||||   ||    || |   | ||||||  | | |||||   |   || ||| |  ||  |   |     |    | |  ||  | |  |||   |  | | | || | |  |  | ||||  |                      
TATGGACTATGCATTTGAGTTCATTATCAACAATGGCGGCATTGATTCTGAAGAGGATTACCCTTACCGTGGTGTTGATGGTAGATGTGACACATATAGGgttagtaacttggtcctgattatttgatgacaatcaatgcttataaaagatatttatcactcaaattcttattgttttttctatgtttggttattttgcttttgcgcag

upper sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv03s0180g00010.t01 (Vitis vinifera), 5'ss of exon 2
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggtagtagcataat-tttgatatgctattgc--tcacttgtgctgctatac--tcacag---------------------------------------
 ||||||||||| ||||| |||||||||||||||||||| || || | ||| || || |||||||||   |     ||   |   |||||    ||| |||| | |  | ||  |     |  ||||     | |   | |  ||   |   ||| | | | |||   |||         | ||    |   ||                                       
CATGGACTATGCTTTTGAATTCATCATCAACAATGGTGGCATTGATAGCGAAGAAGATTACCCTTACCGGGCGGCTGATACAACCTGTGATCCTAACCGGgtttgtgccttcaccaa-attttcttgaagagtgaaaaattttcaagttgcctgaaagggtgttgtgttcatggacatgaccatgaggttgtagtataatcctaattcactgtaatatatttccttctttcag

upper sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S49_32V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgta---tctttcgtctt--ctttgctcccttggtttttcaggtagta----gcataattttga-------tatgctattgc-tcacttgtgctgctatactcacag-------------------------------------------------------------------------------------
 ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||| |  |  || |  |  ||||| |    |||||||   |||   || ||   |||   |  |||  ||   | ||  |      || |||||  |       ||   |||    | |  | ||    | |  || |||                                                                                     
TATGGATTATGCGTTTGATTTCATCATCAAAAATGGTGGAATCGATACCGAGGAGGACTACCCCTACAAGGCAACTGATGGCCAATGTGATGAGGCCAGGgtaaactctaatgttttgattttctccatttgaattactacgttatgttttacaaaatttcaacggtgattagtttatcatgtgaggtatggcattttgttcgcagatttagccagaatttggcattcatttgcatcttggtgttgttcgatttctctcagaatcttattagtgacgattctctcttgcag

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|86906070|gb|CI292601.1|CI292601
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|86830251|gb|CI290403.1|CI290403
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|29617445|gb|CB622457.1|CB622457
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|33797168|gb|CF324448.1|CF324448
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACCAAAATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|29681379|gb|CB677654.1|CB677654
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|2800945|gb|AA754239.1|AA754239
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGMCAGCTACGGRGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|58591175|gb|CF989483.1|CF989483
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|33364707|gb|BP433017.1|BP433017
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|86847823|gb|CI288863.1|CI288863
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAGACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|14571289|gb|BI118657.1|BI118657
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
EST: gi|29641659|gb|CB646666.1|CB646666
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTA
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTA
EST: gi|14571385|gb|BI118753.1|BI118753
EST:     AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGG                         AAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC
genomic: AGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAAC

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), 75 (downstream exon)
Score: 140

GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcg ... atactcacagAAAAACGCAAAGGTTGTCACAATTGACAGCTACGAAGATGTAACACCAAACAGTGAGACGAGTCTGCAGAAGGCGGTAGCAAACCAGCCCGTCAGTGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggtagtagcataattttgatatgctattgctcacttgtgctgctatactcacag

- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG