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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataagcacagctctgagctattgcagtgcatatatcagattcaactccatcttatgaattacacgcatttcatttatctcccttgttaactgtgacaattatgtagcaagggttattatcctgaactttgttagctaaattgccctaacatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g20640.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 8
gtataagcacagctctgagctattgcagtgcatatatcagattcaactccatcttatgaattacacgcatttcatttatctcccttgttaactgtgacaattatgtagcaagggttattatcctgaa---ctttgttagctaaattgccct--------aacatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG
                                                                                            | | | | | || ||||||| | | ||||| ||||   ||| ||   | |   |   ||        ||||| ||||||   |||   | ||     | | ||| || ||||||| |||||||||||| | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||  | |||||||| ||||| ||||
--------------------------------------------------------------------------------------------tattata-taatatagcaagagctgttatcatgaataccttagtcctccaggatatactcttccacaaacatttcctgaatgactagctgtct---ctgtgcagGTTCTTCCAGGGATGATGGGTTTCCTCGCGTACAAGGCTGCAGCTTTGGTTCAAGTCTACAGAGACAACGAGGACCTCCGCTTGATACTTCCTGATGAAG

upper sequence: LOC_Os03g20640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G018678_T01 (Zea mays), 3'ss of exon 8
gtataagcacagctctgagctattgcagtgcatatatcagattcaactccatcttatgaattacacgcatttcatttatctcccttgttaactgtgacaattatgtagcaagggttattatcctgaa---ctttgtt--agctaaattgcccta---acatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG
                                                                                            | | | | |    ||  ||| | | ||||  | ||   ||| ||      || |||   | |   | || ||||||   |||   | || |    || ||| || ||||||| |||||||||||| | |||||||||||||| |||||||| || |||||||| || || ||||| ||  | |||||||| ||||| ||||
--------------------------------------------------------------------------------------------tattatattctaatatgaagagctgttataataaataccttagtctagattatattcttccacacatatttcctgaatgactaactgtctttaa-atgcagGTTCTTCCAGGGATGATGGGTTTCCTCGCATACAAGGCTGCAGCTTTGGTTCAGGTCTACAGAGATAACGAGGATCTCCGCTTGATACTTCCTGAGGAAG

upper sequence: LOC_Os03g20640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G055606_T01 (Zea mays), 3'ss of exon 6
gtataagcacagctctgagctattgcagtgcatatatcagattcaactccatcttatgaattacacgcatttcatttatctcccttgttaactgtgacaattatgtagcaagggttattatcctgaa---ctttgtt--agctaaattgcccta---acatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG
                                                                                            | | | | |    ||  ||| | | ||||  | ||   ||| ||      || |||   | |   | || ||||||   |||   | ||    |||| ||| || ||||| | |||||||||||| | |||||||||| ||| |||||||| || |||||||| || || ||||| ||  | |||||||| | ||| ||||
------------------------------------------------------------------------------------------cttattatattctaatatgaagagctgttataataaataccttagtctagagtacattcttccacacatatttcctgaatgactaactgtct---ttatgcagGTTCTTCCAAGGATGATGGGTTTCCTCGCATACAAGGTTGCAGCTTTGGTTCAGGTCTACAGAGATAACGAGGATCTCCGCTTGATACTTCATGAGGAAG

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|88468425|gb|CI514907.1|CI514907
EST:     GTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88511325|gb|CI438831.1|CI438831
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|29663267|gb|CB659542.1|CB659542
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88513676|gb|CI441182.1|CI441182
EST:     NATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTNTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTGTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88209249|gb|CI208675.1|CI208675
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88377953|gb|CI501222.1|CI501222
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88477015|gb|CI414286.1|CI414286
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|86418084|gb|CI032293.1|CI032293
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88468760|gb|CI502167.1|CI502167
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTGCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88511424|gb|CI438930.1|CI438930
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88283617|gb|CI405063.1|CI405063
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88418720|gb|CI506481.1|CI506481
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88508429|gb|CI435935.1|CI435935
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88295578|gb|CI530141.1|CI530141
EST:     GATTNTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88526125|gb|CI452504.1|CI452504
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATNGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|89170010|gb|CI039287.1|CI039287
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88477016|gb|CI414287.1|CI414287
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88982477|gb|CI027950.1|CI027950
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|86871982|gb|CI332154.1|CI332154
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|88491158|gb|CI428430.1|CI428430
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGGATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
EST: gi|14571326|gb|BI118694.1|BI118694
EST:     GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAG                         CTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA
genomic: GATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTA

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: 70 (upstream exon), 69 (downstream exon)
Score: 52

TTCAGTAGCTCTTTCGTCTCCAAGGCTTGTGATACCCGCTATATTTTTTGGATTGTCAACCTTGTCAGATCACTTTCAAAATAGCATTTTAAATTTTGAGgtataagcac ... ccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttagctaaattgccctaacatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG
              ccctaac  putative branch site (score: 52)
                                  ctgtttctcctcctta  putative PPT
       taaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagcacagctctgagctattgcagtgcatatatcagattcaactccatcttatgaattacacgcatttcatttatctcccttgttaactgtgacaattatgtagcaagggttattatcctgaactttgttagctaaattgccctaacatgtcctgagcaactgtttctcctccttatacagCTTGTTCCAGGAATGATGGGTTTCTTTGCATACAAGGCTGCCGCTTTGGTACAAGTCTACAGGGACAATGAGGACCTTAGATTGATACTGCCTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG