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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgattattttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA

Basic information

species Oryza sativa
transcript LOC_Os08g09240.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134613_T01 (Zea mays), 3'ss of exon 2
gtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgatta-ttttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA
|||||     |   |  || || |   ||   |  | ||| ||   ||||||   ||||||  | ||   || |  ||| ||    |  |||||||||||||||||||||||| |||||||||||||| || ||||||||||| || ||
gtaagcc--ttaattaatttttacccatgtcctctgattatttc--catgatagcttttgtgttcattcaaacctgctttct----tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134613_T04 (Zea mays), 3'ss of exon 3
gtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgatta-ttttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA-----------------------------------------------
|||||     |   |  || || |   ||   |  | ||| ||   ||||||   ||||||  | ||   || |  ||| ||    |  |||||||||||||||||||||||| |||||||||||||| || ||||||||||| || ||                                               
gtaagcc--ttaattaatttttacccatgtcctctgattatttc--catgatagcttttgtgttcattcaaacctgctttct----tgtaatatagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAGTCAGCCATTTCACGAGTATCTCTTTAGTGCATTTGTATTTTCTCTA

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G014975_T01 (Zea mays), 3'ss of exon 1
gtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgat-ta--ttttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA
|||||     |   |  |||||     ||   |  | | | |||  || ||| ||  ||||||||| ||   || |   |           ||| |||||||||||||||||||| |||||||||||||| || ||||| ||||| || ||
gtaagcc--ttaagtaattgttatccatgccctctgatcatttt-ccacgatatagcttttgttctcatccaaatcgggt-----------aatgtagGTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATCGACAAGAAAAA

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttggatggattcttgttgcttgtggtgtt------cgcttactttgtcatgattattttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA
||| |     ||  |   |            |||      ||  |  | ||| |||  | | |   | || | |      | ||  | || |   |||||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||||
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttt-tctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA

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|33659136|gb|CF281749.1|CF281749
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|33657525|gb|CF280139.1|CF280139
EST:     AGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: AGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|88963125|gb|CI026798.1|CI026798
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|88974162|gb|CI002783.1|CI002783
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|89168539|gb|CI038893.1|CI038893
EST:     CATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: CATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|88833607|gb|CI077088.1|CI077088
EST:     ATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: ATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|33671347|gb|CF299586.1|CF299586
EST:     GCAGGCTGAGGCCAACCGCNATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GCAGGCTGAGGCCAACCGC-ATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|58590250|gb|CF988558.1|CF988558
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|58586677|gb|CF984985.1|CF984985
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|163926759|gb|EG715047.1|EG715047
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
EST: gi|218487512|gb|FG953689.1|FG953689
EST:     GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCT                         GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG
genomic: GGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAG

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: 56 (upstream exon), 53 (downstream exon)
Score: 139

AAAGGAGGCAGGCTGAGGCCAACCGCATCAGGGAGAAGTATCCCGATAGAATTCCTgtaagttgga ... ttaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtcatgattattttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA
          attattttgttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggatggattcttgttgcttgtggtgttcgcttactttgtcatgattattttgttcttatgtgaagcaacttcctgtgattaaatatagGTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA