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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttctgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G106703_T02 (Zea mays), 3'ss of exon 8
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttct-gttttaacatcccaatcacatgcc-ccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
|| ||   ||| |||   |||   |    ||     | || | | | ||||   |     |||| ||  |   | ||| |    || ||    ||||          |  ||  ||||| ||    || |   ||| |  |||   | |||    ||| |  | |    |  ||| ||     |||||||||||||  ||||||||||||| ||||| ||||||||||| ||| |||| || |||||
gtttgtgtattatttggtactctgtatacttcacgttcca-ttatttttcacctgttacctgttccttatgcgagcatactctacatatattgccatttcttgtccctctttctattttttttaatttattgccatttctttttcgtgtttctattttttgttccttcctgtttaaat-----ttcagaagGATACTGAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAG

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G059018_T01 (Zea mays), 3'ss of exon 8
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttc-tgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttc-gcattaattatatcatt--tttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
                    ||| ||  | || ||  | | |   ||||   |    || |||| | || |||  || |     |   |     |||  |   ||||| | | | ||  ||||     || | |||    || | |  || |||||| || ||  | | | |||   |  |   ||||||||||||||  | ||||||||||| ||||| |||||||||||||||||||| || |||||
-------------------gttcgttattattatttggtactctttattattacacttaatgttccatgatttttcaccagctacctgtttttaatgcgggcatatttgtgtgacttcattgc-----tgcatatcgccatt-tcttgttcctgtttctatttttgtacttattcctttctaaatttcagAAGGATACTGAGAAGGCAATGAGGATGACTACAAGGCAAACATTAGCTGAGATATGGAG
















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:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29646262|gb|CB651269.1|CB651269
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|33683081|gb|CF311320.1|CF311320
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29661210|gb|CB657485.1|CB657485
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AACGATACGCAAAAGGCAATGAGAATG
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATG
EST: gi|86494625|gb|CI137258.1|CI137258
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         -AGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86499881|gb|CI142514.1|CI142514
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACCAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|87015826|gb|CI279578.1|CI279578
EST:     GCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: GCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29639863|gb|CB644872.1|CB644872
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACTAATAGAG                         AAGGATCCGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|218485410|gb|FG945021.1|FG945021
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29661211|gb|CB657486.1|CB657486
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86500551|gb|CI143184.1|CI143184
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86502542|gb|CI145175.1|CI145175
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86859418|gb|CI278837.1|CI278837
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29680568|gb|CB676843.1|CB676843
EST:     CTGGTGCTACATGCCCTCTAGATGTTGGTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGTCCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86493384|gb|CI136017.1|CI136017
EST:     TCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGNCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: TCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|87019187|gb|CI277903.1|CI277903
EST:     TGGTGCTACATGCCCTCTAGATGTTGCTAAGACCAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: TGGTGCTACATGCCCTCTAGATGTTGCTAAGA-CAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|29677505|gb|CB673780.1|CB673780
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86600100|gb|CI258440.1|CI258440
EST:     TGGTGCTACATGCCCTCTAGATGTTGCTAAGACCAAGGAGACCAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: TGGTGCTACATGCCCTCTAGATGTTGCTAAGA-CAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|86494335|gb|CI136968.1|CI136968
EST:     CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|33683082|gb|CF311321.1|CF311321
EST:     CTGGTGCTACATGCCCTCTAGATG-TGCTAAGACAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAAGGCAAACATTAGCTGA
genomic: CTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCAC-AAGGCAAACATTAGCTGA
EST: gi|88197385|gb|CI196692.1|CI196692
EST:     TGGTGCTACATGCCCTCTAGATGTTGCTAAGACCAAGGAGACAAATAGAG                         AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: TGGTGCTACATGCCCTCTAGATGTTGCTAAGA-CAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
EST: gi|25807715|gb|CA763676.1|CA763676
EST:     AGACAAGGAGGCAACTAGAG                         AGGGATCCGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT
genomic: AGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGAT

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: 64 (upstream exon), 59 (downstream exon)
Score: 92

TGTGCTGGGTGCAAACTTTGCAGCTGGCTTTGTAGCAGGTAGTCTTGCTGCTGGTGCTACATGCCCTCTAGATGTTGCTAAGACAAGGAGACAAATAGAGgtctgcacat ... catttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG
                                 cattaat  putative branch site (score: 92)
                                            tcatttttc  putative PPT
                                  attaattatatcattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcacattctttcccacttccttcgtttttttctgcaataaatattcaaaagaatattgtttctgttttaacatcccaatcacatgccccatggtgcactatttatttaattttcttgccattgtgtacatcttgtttgtttcttttctgtttatacttcgcattaattatatcatttttcagAAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG