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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g11440.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 3
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
||    || ||| ||| | ||||  || ||| || |||||   | | |||   |     |||  | ||| || |||| |  |||||||||||||||| |||||||||||| ||||| || |||||| ||||||| |||||||| ||||| ||||||||||||||| ||||||||||||||||||
gtacacacctcatttctaatgctgcagtaagttatatcttctgtatgtgtaact---gctaatgtattt-tactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 3
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttag-cattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
||  | || ||| ||||| |||| ||| |||  |  ||||   ||| | ||| ||     | |  | ||| ||||||| |  |||||||||||||||| |||||||||||| ||||| || |||||| ||||||  |||||||| ||||| ||||||||||||||||||||||||||||||||||
gtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattt-tattgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 4
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctt-tggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTC---TGGCCATTCTGTTCCTGTTGGTGGTCTTG
    | |||| |  |  |     ||    | || | |        |||   | | |  |||   |     | ||  || |  ||| | || |||||||||||||||||||||||||| || || ||  | || || |||||||||||||| || ||   ||| || |   | |||||||||||||   
----gtacttgagcttta--agcttgtatacatgagttgcggtcattttcttctggtgttatactaacaattttatttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC---

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g00710.t01 (Vitis vinifera), 3'ss of exon 2
----gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctt-tggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTC---TGGCCATTCTGTTCCTGTTGGTGGTCTTG
      |  | |    |  |       ||    | || | |        |||   | |||  |||   |     | ||  || |   || |  | |||||||||||||||||||||||||| || || ||  | || || | |||||||||||| || ||   ||| || |   | |               
tatatcccaagcacttaagctttaagcttgtatacatgagttgcggtcattttcttctagtgttatactaacaattttatttcttatagttgttatacagGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGAAAGTTGAAGGAATCTGAATATTCAGATGGTCAATACATCC---------------

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 3'ss of exon 1
--gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGC---CATTCTGTTCCTGTTGGTGGTCTTG
      || ||| ||      ||  |   || | |       |  | ||   || |   | |||||  ||| |     | |  ||| | || |||||||||||||||||||||||||| || || ||  | || || |||||||||||||| || || |||   || |   | |||||||||||||   
gtactggagctttaagct---tgtatacacaggttggggtcattttcttctggtgttatactaacaattttat----ttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCAGGCGGTCAATACATCCCTGTTGGTGGTC---

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|27577737|gb|CB000432.1|CB000432
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|29627509|gb|CB632520.1|CB632520
EST:     TTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTGGTCAACCTTATTGGGAAA
genomic: TTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|699763|gb|D46054.1|D46054
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGNGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|58679189|gb|CK067876.1|CK067876
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|27554203|gb|CA998103.1|CA998103
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|29665157|gb|CB661432.1|CB661432
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|33796315|gb|CF324025.1|CF324025
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA
EST: gi|2797483|gb|AA750777.1|AA750777
EST:     CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTCCTGGTCAACCTTATTGGGAAA
genomic: CCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAA

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), 75 (downstream exon)
Score: 73

CGGTCAACAAGGCTCATACCCAATTAAGCTGTTCTACACTTCAAACATGCCCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaactt ... gctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
                           cattaac  putative branch site (score: 73)
                                           ttgcttt  putative PPT
     aatctttaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG