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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtag

Basic information

species Oryza sativa
transcript LOC_Os05g06430.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G008647_T04 (Zea mays), 5'ss of exon 1
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaat---acttaaatttacataatccaattccaatataatctattggtt-gcttctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || ||||||||||| | | | | |     |  | | |    |   | | || || |   | |     ||  ||  | ||| ||  || | | ||||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGACTTCAGAGgttg-gttataaagccaagcgaaatcgctttggaatcaagttgatgaattatggatctgatgcattctgttcatttgttgctgtgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G008647_T02 (Zea mays), 5'ss of exon 5
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaat---acttaaatttacataatccaattccaatataatctattggtt-gcttctgtag-------
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || ||||||||||| | | | | |     |  | | |    |   | | || || |   | |     ||  ||  | ||| ||  || | | ||||         
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGACTTCAGAGgttg-gttataaagccaagcgaaatcgctttggaatcaagttgatgaattatggatctgatgcattctgttcatttgttgctgtgtaggctag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G404011_T01 (Zea mays), 5'ss of exon 6
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaat---acttaaatttacataatccaattccaatataatctattggttgctt-ctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || ||||||||||| | | | | |     |  | | |    |   | | || || |   | ||    ||  ||  | ||| ||  ||  || ||||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGACTTCAGAGgttg-gttataaagccaagcgaaatcgctttggaatcaagttgatgaattctggatctgatgcattctgttcattttttgctgtgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AC217311.3_FGT007 (Zea mays), 5'ss of exon 2
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaat---acttaaatttacataatccaattccaatataatctattggtt-gcttctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || ||||||||||| | | | | |     |  | | |    |   | | || || |   | ||    ||  ||  | ||| ||  || | | ||||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGACTTCAGAGgttg-gttataaagccaagcgaaatcgctttggaatcaagttgatgaattctggatctgatgcattctgttcatttgttgctgtgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G170845_T01 (Zea mays), 5'ss of exon 4
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaat---acttaaatttacataatccaattccaatataatctattggtt-gcttctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||| | ||| ||||||| || || ||||||||||| | | | | |     |  | | |    |   | | || || |   | ||    ||  ||  | ||| ||  || | | ||||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCTGGGATACAAAGGGCCACCTGACTTCAGAGgttg-gttataaagccaagcgaaatcgctttggaatcaagttgatgaattctggatctgatgcattctgttcatttgttgctgtgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G138616_T01 (Zea mays), 5'ss of exon 1
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtag
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || |||||||||||  || || || |   |||  |  |   |  |  |||| |  |  |    |                              
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGACTTCAGAGgt--tggttataaagccaagcgaaatcgct-ttggaattcatttgttgttgtgtag--------------------------

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G110742_T02 (Zea mays), 5'ss of exon 8
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatata---gaaggtacttaaatacttaaatttacataatccaattccaatataatctattggtt-gcttctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||| ||||||| || || ||||||||||| |  | |  |   |   |||    |||    | | || || |   | ||    |   ||  | ||| ||  || | |  |||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGTCGGGATCCAAAGGGCCACCTGACTTCAGAGgttggtcataaagccaagcgaaatcgctttgg-aatcaagttgatgaattctggatttgatgcattctgttcatttgttgttgtgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 8
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatata---gaaggtacttaaatacttaaatttacataatccaattccaatataatctattggt-tgcttctgtag--
||||||||||||||| || || || ||||||||||| |||||||| ||||||||||| ||||| |||||||| ||| ||||||| || || | |  |||||| |    |  |  ||   |||    |||    |   || || |   | ||    ||  ||  | ||| ||  | || | ||||    
TGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAGTTCATTAATGAGAAGTGTGGCACCAGCCGGGATCCAAAGGGCCACCTGAATCAAGAGgttggttataaagctaagcgaaatcgctttgg-aagcaagttgatgaattctggatctgatgcattctgttcatgtgttgctgtgtag

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|58675064|gb|CK063751.1|CK063751
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|163927756|gb|EG710536.1|EG710536
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|163922917|gb|EG712742.1|EG712742
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58653948|gb|CK042628.1|CK042628
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58672427|gb|CK061113.1|CK061113
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58676547|gb|CK065234.1|CK065234
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|86513133|gb|CI155766.1|CI155766
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|163925853|gb|EG714953.1|EG714953
EST:     AGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: AGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|11026410|gb|AU163011.1|AU163011
EST:     GGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: GGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA

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: 56 (upstream exon), 73 (downstream exon)
Score: 96

TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAGTTTATTAATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT