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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G106703_T02 (Zea mays), 5'ss of exon 7
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
 |||||||||||||| ||| ||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| |||| |  |||   | |   | | | |  |   |  | |||| |||  | |||||    |||| || |  | |||    | | ||       |||| |  || ||| ||   | |||||
TACAAAATTATCGTGTTCTGTGGACTGGGGTGGGTGCACAACTGGCTCGAGATGTTCCTTTCTCCGCTATATGCTGGTCAACTCTTGAGCCTgtaagtttctgccttcttggtca-tgg--aaactcctatttgttaa-atccatgc----atcacttccagagttc--catgacatcg-----atctcactttgctaacaccatgtgcag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G059018_T01 (Zea mays), 5'ss of exon 7
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
 ||||||||| |||| ||| ||||| || |||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||| |||| |  |||  || |   | | | |  |   |  | |||| |||  | ||||||    ||| ||          |  | | || |     |||| |  |||||| ||   | | |||
TACAAAATTACCGTGTTCTGTGGACTGGGGTGGGTGCACAACTTGCTCGAGATGTTCCTTTCTCTGCTATATGCTGGTCAACTCTTGAGCCTgtaattttctgccctcttggtca-tgg--aaactcctatttgttaa-attcatgcc----tcactt----------tcatgacatga-----atctcactttactaacaccatgttcag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G41650.1 (Glycine max), 5'ss of exon 7
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtc--acttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
 ||| |  ||||||  |   ||||| ||| | || ||||||||| |||| |||||||| | ||||||||| ||||||||||| || ||||| || |     ||||   |   | | |  |  |     |  |||   |    ||  |    |||| || || | | ||      |   || |  |                            
TACATAGGTATCGTTTTTGGTGGACTGGTCTTGGAGCACAACTTTCTCGTGATGTTCCATACTCTGCTATTTGCTGGTCAACCCTTGAGCCAgtgagattttgttacatttaattaaaaaaatgaaaatgagttgattttattgtgtttgggtattatgtgttgactttggag-atgctttacag----------------------------

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G44250.1 (Glycine max), 5'ss of exon 7
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
 ||| |  ||||||      ||||| ||| | || ||||||||| |||| |||||||| |||||||| || ||||||||||| || ||||| || |       || ||| || |             ||  ||   ||  || |    ||| | ||||     |||   ||||   || |||    ||| ||||   | | |  | |||||
TACATAGGTATCGTTTCTGGTGGACTGGTCTTGGAGCACAACTTTCTCGTGATGTTCCATTCTCTGCAATTTGCTGGTCAACCCTTGAGCCCgtgag-----attttgttacat-------------ttaattaaaaaaatgaaaaggagt-tgattttt---attttgtttagggtttatg---ccttgactttggagc-tgctttgcag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv16s0050g02360.t01 (Vitis vinifera), 5'ss of exon 8
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
  |  |  || ||||  || ||||| ||  | || |||||||||||||| ||||||||||||||||| || || |||||||| |||||||| ||||  |  ||||||       ||| ||||  ||||     |||   ||  |||    || |      |   || ||  |||  ||  |  | || |     ||               
TGCGGAGCTACCGTGTCCTGTGGACAGGCATTGGAGCACAACTTGCTCGTGATGTTCCTTTCTCTGCAATTTGTTGGTCAACCCTGGAGCCAgtaagactttgttcttcttaacagttgttaaatttta--cagctgcagtctatgtacctaacgcacatt---tttatgctaa--tttcttttctcctcctgcacag-------------

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv15s0046g01370.t01 (Vitis vinifera), 5'ss of exon 7
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag
  |||| ||| ||||   | ||||| ||  | || || ||||| ||||| |||||||||||||| || || |||||||||||||| ||||| || |  ||   |||| | |   || ||||   |   |  |     |  |   |     |||| ||    | || || |      ||| | || ||||   || | ||    ||||||||
TTCAAAGTTACCGTGTCTTGTGGACTGGCCTTGGAGCGCAACTCGCTCGCGATGTTCCTTTCTCCGCAATCTGCTGGTCAACACTTGAGCCAgtgagacctcattctctaa---agcagtttcatggatagt-----acatatctaattatatctttccacacatccaatcct---ttacttgtttctttttttcccat----gtatgcag

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|66925835|gb|CX112683.1|CX112683
EST:     GCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: GCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29646262|gb|CB651269.1|CB651269
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|33683081|gb|CF311320.1|CF311320
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29661210|gb|CB657485.1|CB657485
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29639863|gb|CB644872.1|CB644872
EST:     TTGCTCGGGATGTTCCTTTCTCTGGTATATGGTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGATAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|218485410|gb|FG945021.1|FG945021
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29661211|gb|CB657486.1|CB657486
EST:     ATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: ATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29680568|gb|CB676843.1|CB676843
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|218496315|gb|FG954193.1|FG954193
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29677505|gb|CB673780.1|CB673780
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGT
EST: gi|29677504|gb|CB673779.1|CB673779
EST:     TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCG                         ATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTA
genomic: TTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTA

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), 72 (downstream exon)
Score: 67

CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccct ... ttgtatgcagATTCGAAGAAAGCTGCTTGGTATCGTCGGAGAAGAAGGTGATGCAGCTAGTGTGCTGGGTGCAAACTTTGCAGCTGGCTTTGTAGCAGGTAGTCTTGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAAATTATCGTGCTCTTTGGACGGGTGTGGGTGCACAACTTGCTCGGGATGTTCCTTTCTCTGCTATATGCTGGTCAACACTGGAGCCGgtaaatccctgttctgtcacttagtagttatgtttttgtttgctaatgtgcatgccagtatcatttgctaaattcattttaaaattaatggtatcttaacttactatcattgtatgcag

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