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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacatttcatcttgacaaaccatcaattttctatatttctctcataacttacttataggttcctgacttcttcctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
GGCTCAGCCCCCGTC---AAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacat--ttcatcttgacaaaccatcaattttctatatttctc--tcataacttacttataggttcctgacttcttcctgcag
    ||| | || ||   ||||  |||||  |||| ||||||||||||||||| |||||| |||| ||| |||| ||||| || ||||||||||| ||||| ||||    |||   |  | |||||||||   |||    |  || | |     |   |||       || |||| |      ||| |||||
---ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
--GGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacatttcatct-tgacaaaccatcaattttctatatttctctcataacttacttataggttcctgacttcttcctgcag----------------------------------------
    |||| |   | |||    |||| | || ||||| |||||  | ||||| ||| || |||||||| |||| ||||| ||||||||||| |||||||| ||||           ||   ||| |||   | | || |   |  |||  | | | |  | || |   |    |  |  || |   |                                         
ATTTCTCATCATTCCTCACA--CCCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaagcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcg-aattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 2
GGCTCAGCCCCCGTCAAGGC-----CCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacatttcatcttgacaaacc----atcaattttctatatttctctcata--acttacttataggttcctgacttcttcctgcag-----
     | | | | ||||  |     |||  |||| ||||||||||| || ||||| ||| |||||||  || |||| ||||| || ||||||||||||||||| ||||| |    |||  |  | ||  |       | |||| |  || | ||  |  ||  | |  | | |   |     | || ||  | ||      
-----AACTCTCATCAACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAGGGCTGTTGCTGCACACCCCTGGCATGATCTTGAGATAGgtaccta--cttttgttgtaacgcatgttgagttaattcttaatgtctcctttttactagtggccttttattatgacattttttatttcaatgcag

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|88381548|gb|CI682205.1|CI682205
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88720264|gb|CI743563.1|CI743563
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|4878573|gb|AU062872.1|AU062872
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88725059|gb|CI748318.1|CI748318
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|58598649|gb|CK009177.1|CK009177
EST:     ATGTCCCGGAGATCTATTGCCGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: ATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88396360|gb|CI598472.1|CI598472
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|33663512|gb|CF294479.1|CF294479
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|699797|gb|D46088.1|D46088
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|86831354|gb|CI297623.1|CI297623
EST:     GATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88300593|gb|CI587397.1|CI587397
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCAC-AACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88400835|gb|CI616840.1|CI616840
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88425227|gb|CI564744.1|CI564744
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88300279|gb|CI584698.1|CI584698
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|3759881|gb|C97139.1|C97139
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88578597|gb|CI687538.1|CI687538
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC
EST: gi|88325992|gb|CI651039.1|CI651039
EST:     TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTG                         GACCTGGTGCACCAACTATATTCAACTGC
genomic: TATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC

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: 62 (upstream exon), 71 (downstream exon)
Score: 41

GGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgaca ... cttcctgcagGACCTGGTGCACCAACTATATTCAACTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCAGCCCCCGTCAAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacatttcatcttgacaaaccatcaattttctatatttctctcataacttacttataggttcctgacttcttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC