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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctgttactgcagttcatatttgtcaatataattcttttttgtcaatatttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA

Basic information

species Oryza sativa
transcript LOC_Os02g38080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G165231_T01 (Zea mays), 3'ss of exon 4
gtttctgttac-tgca-gttcatatttgtcaatataattcttttttgtcaatatttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
||||||  | | | ||  ||  || ||    |     |  |||| ||| | ||||     | ||||  |  | |  |||||||||||||||||| ||| |||||||||||||||||||||||||||| || |||||||| || || ||||||||||||||||| ||||||||||| ||||
gtttctactgcatccatatttttagtttctgagtccttaattttctgt-attattaatgtaacctgggaattctaaacagTTGTACAGCACAGTAACACTGAGGCATGGAGAAAAGAAGCATTACAACCACAAAGTAGATGTCTACAGCTTTGCAATTGTGTTGTGGGAACTCCTCCACA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G36210.1 (Glycine max), 3'ss of exon 4
--gtttctgttactgcagttcatatttgtcaatataattcttttttgtcaatatttgctaatc--ctgaaat----atatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
   | |     | | ||     | | |||   |    | | | ||| | |  || |    |     |  |||    | |    |||||||| || || || ||| | ||||| || || |||||||||||||| |||||||| || | |||||| |||||||||||||| ||||| ||| | ||||
gtatattgacaaatacatgcattttctgtgtcttctctccatatttatgagcatctatggactgattacaatgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 4
----gtttctg--ttactgcagttcatatttgtcaatataattcttttttgtcaatatttgctaatcc---tgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
     ||  ||  |   | || ||  | | | |       ||  ||||  |    |||   || ||     ||| | | ||   |||||||| || || || ||| | ||||| || || |||||||||||||| |||||||| || | |||||| |||||||||||||| ||||| ||| | ||||
gtatattgatgaatagattcactttctctgtcttctctccatatttttgagcatgtatggactgattacagtgacaaaaattt-cagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 4
-gtttctgttactgcagttcatatttgtcaatataat----tcttttttgtcaatatttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
  | |   |||||      |||||||||  || |  |    |  | ||||  | |    |  |||| ||    |     ||||||||||||||| || ||  |  |    ||||| |||||||| |||||||||||||| ||||  |||||||||||||| ||  | ||||| ||  | ||||
gttcttctttacttatagacatatttgttcatttcttgtgcttctctttgctacttaaagacaatcttggtggaatattacagTTGTACAGCACGGTAACTCTTCGATTGGGAGAGAAGAAGCACTACAATCATAAAGTCGACGCCTATAGCTTTGCAATAGTTCTTTGGGAGCTTTTACACA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G27560.1 (Arabidopsis thaliana), 3'ss of exon 4
--gtttctgttactgcagttc--atatttgtcaatataattcttttttgtcaatatttgctaatcctga--aatatatc-cacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
     | | ||||| |    |    |||| ||  |    |||    |||||  |  | |   ||| ||   |||  ||   |||| | ||||| || || || || ||||| ||||| ||||| || || |||||||||||||| | ||| |||||||| ||||| || ||||||||  ||| ||
gtaactatattactactaacccgggatttttcttttcttttcgcggttgtc--ttatcggacatcttggttaatgaatgatacagCTCTACAGTACGGTTACGTTAAGGCAAGGAGAGAAGAAACACTATAATCATAAAGTAGATGCTTACAGCTTTGCCATTGTCTTGTGGGAACTTATTCTCA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g09290.t01 (Vitis vinifera), 3'ss of exon 4
-------gtttctgttactgcagttcatatttgtcaatataattcttttttgtcaat----atttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
       |||      | ||||       ||||| | | |  || | | | | || |    |      ||   ||  || |     ||||||||||| || |||||||| ||||||||||| |||||||| |||||  | ||||| || | |||||||||||| ||||| || ||||| ||  | || |
gtactttgttcagaaaaatgcatgcttcttttgttattttgcttttctgtggccacttcagaaccatgaactttgttatctggtggcagTTGTACAGTACTGTGACATTAAGGCATGGAGAGAAGAAGCACTACAACAACAAAGTGGATGCTTATAGCTTTGCCATTGTCTTGTGGGAGCTTTTACATA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g00370.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtttctgttactgca---gttcatatttgtcaatata-----attcttttttgtcaatatttgctaatc--ctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
                | || | ||  | ||    || || |||||   |  |     |       |    |||  |  | | ||  ||   |  |      || | || |||||||| ||||||||||||||||| ||||||||||||||||| || || || |  || |||||||| |||||  | ||||||||| |||| |
gtacttaacacttaatgcttttatttattcattcatttatttttgttggtgaatggggaaggggactccagaatgctgaccattcacctttcactttgttgtagCTTTATAGCACAGTAACATTGAGGCATGGAGAGAAGAAGCATTACAATCACAAGGTGGATGCCTACAGCTTTGCTATTGTACTGTGGGAACTCGTTCATA

upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ07184 (Selaginella moellendorffii), 3'ss of exon 4
gtttctgttactgcagttcatatttgtcaatataattcttttttgtcaatatttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
      || |     | || |||   | ||| |     ||| |  | ||      |     ||   |      | ||| | |||||||| |||||  | ||  | || |||||||||||||| ||||| || || ||||| || ||||||||||| ||||| ||||| || ||   ||
------gtcagatatgctcttatccat-aatcttccattttgtactaaaacaaaaccttctcttttactccctcgcagCTCTACAGCACGGTGACGCTAAGAAACGGCGAAAAGAAGCATTATAATCAAAAGGTGGACGTCTACAGCTTTGCAATCGTGTTGTGGGAGCTGCTGACCA

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|29672964|gb|CB669239.1|CB669239
EST:     GCAGAGACAGGAACATACCGTTGGATGGCTCCAGAG                         TTGTACAGCACAGTGACA-TGAGGGCATGGAGAAAAGAAGCATTACAATCA
genomic: GCAGAGACAGGAACATACCGTTGGATGGCTCCAGAGgtttctgtta ... atatccacagTTGTACAGCACAGTGACATTGA-GGCATGGAGAAAAGAAGCATTACAATCA




















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: 73 (upstream exon), 75 (downstream exon)
Score: 52

GAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGGAACATACCGTTGGATGGCTCCAGAGgtttctgtta ... atatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcaatataattcttttttgtcaatatttgctaatcctgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA
                              tgctaat  putative branch site (score: 52)
     aatataattctttttt  TA-rich tract