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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccagcacacacgcaaacctgggcataaaacgtcacatatatatgataaccaagctgtgatagaaaattatgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC

Basic information

species Oryza sativa
transcript LOC_Os02g48964.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G048045_T01 (Zea mays), 3'ss of exon 9
gtatgccagcacacacgcaaacctgggcataaaacgtcacatatatatgataaccaagctgtgatagaaaattatgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC
        | ||    || || |    ||||     |         | | |||   |  | | ||||||     ||    | ||| ||     || ||  ||   |||||   ||| |||    ||||||| || |||||| | ||||| ||    || ||||| |||||||| ||||||||||| |||||  ||||||||||||||||||||||||| ||||||||||
--------gtaccattgctaatc----catatgctttagtgagctcaggttaatagacttttcatagaag----tgctgtaatgatgtg-aatattcaccat--ttggtt---ttgcttctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109039_T04 (Zea mays), 3'ss of exon 3
gtatgccagcacacacgcaaacctgggcataaaacgtcacatatatatgataaccaagctgtgatagaaaattatgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC
        | ||   ||| || |   |         |  |  |  | | |||  |  | | |  || ||| |  |||||   ||     | |      | |  | | |  | ||||||||    |||||||  |||||||| | ||||| ||    || ||||| |||||||| ||||||||||| |||||  ||||||||||||| ||||||||||| ||||||||||
--------gtaccatcgctaatcaatgtgctttttttagctcaagt-taatagact-gttatcgta-aaagtgttgtgatgatgtgaattaggtcatttcaccatttg--attttgtttctggatgcagACAGTTCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACCGGCAACCAAGACAAGACATGCC
















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|86886604|gb|CI322836.1|CI322836
EST:     TTGTGGGNGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|218482014|gb|FG963446.1|FG963446
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29677180|gb|CB673455.1|CB673455
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29671103|gb|CB667378.1|CB667378
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|163922839|gb|EG712235.1|EG712235
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|218488856|gb|FG965224.1|FG965224
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCGTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCC-TTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
EST: gi|29632271|gb|CB637280.1|CB637280
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|23322153|gb|BU572398.1|BU572398
EST:     TGT-GGGGATGATCCTAATGGTTTACTTAATTGCCGCCAATTCAGAAAAG                         ACTTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
genomic: TGTGGGGGATGATCCTAATGGTTTAC-TAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagAC-TCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
EST: gi|25801428|gb|CA757389.1|CA757389
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|58685293|gb|CK073980.1|CK073980
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|86902833|gb|CI312210.1|CI312210
EST:     ATGATCCCTAAATGGTTTTACTTAATTGACGCCAATTCAGGAAAG                         ACTCTTCCATTCCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTT
genomic: ATGAT-CCT-AATGG-TTTAC-TAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTT-CATT-CCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTT
EST: gi|86868119|gb|CI331871.1|CI331871
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|218501212|gb|FG955432.1|FG955432
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|86479527|gb|CI122160.1|CI122160
EST:     TTGTGGGGGATGATCCTAATGGTGTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|86902924|gb|CI312301.1|CI312301
EST:     GTGGGGGGATGATCCTAATGGTTTACTTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
genomic: GT-GGGGGATGATCCTAATGGTTTAC-TAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATT-CCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
EST: gi|27548190|gb|CA766256.2|CA766256
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29619649|gb|CB624661.1|CB624661
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29672639|gb|CB668914.1|CB668914
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|2797334|gb|AA750628.1|AA750628
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|218495836|gb|FG960244.1|FG960244
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|86834405|gb|CI344350.1|CI344350
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACCCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29679291|gb|CB675566.1|CB675566
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|86862373|gb|CI345493.1|CI345493
EST:     TGTGGGGGATGATCATAATGGTTTACTAATTCACGCCAATTCACGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
genomic: TGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCA-GGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTG
EST: gi|38468281|gb|CF952412.1|CF952412
EST:     GATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: GATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
EST: gi|29674117|gb|CB670392.1|CB670392
EST:     TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG                         ACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG
genomic: TTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGG

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), 48 (downstream exon)
Score: 12

CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAGgtatgccagc ... ccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC
                        tgataac  putative branch site (score: 12)
                                  ttactttgtttccct  putative PPT
                       atgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccagcacacacgcaaacctgggcataaaacgtcacatatatatgataaccaagctgtgatagaaaattatgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG