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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgaggcatatctgcatgttctgttgaattcttgagctactgtggcaatattttctagttgtcgtttggctgatttctgattcctgtgatgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g34460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G043737_T01 (Zea mays), 3'ss of exon 3
aactgaggcatatctgcatgtt---ctgttgaattcttgagctactgtggcaatattttctagttgtcgtttggctgatttctgattcctgtgatgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG
 || ||||   |  |  | |||   |  ||   | |      |   ||    |  | ||     |||  |||       ||||  ||||||| |  | | ||||||||||  ||| || || || ||||| ||||||||||| ||| ||||||| ||||||||||| ||||||||||| |||||||| |||||||| || |||
taccgaggagcagattaaagttaaccaattaggtacaaatctttaagttttgaattgttgatactgttatttaat---cttctctttcctgtaacttatgtagGGGCCCAGGTCGTTTTGACGGCGACAGGCCAAGGTTTGGTGACAGGGATGGGTACCGTGGTGGTCCTCGTGGTGCTCCTGGTGACTTTGGTGGCGATAAG

upper sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G050925_T01 (Zea mays), 3'ss of exon 3
aactgaggcatatctgcatgttctgttgaattcttgagctactgtggcaatattttctagttgtcgtt--tggctgatttctgatt--cctgtgatgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG---
 ||||||| |||| |  | |  ||    | || |  |   | |||   | | |||  | ||||  | |  |   | || |    ||  | ||| |||| | |||||||||   ||| || ||||   |||||||||||||||||||| ||||||  ||||||||||| ||||||||||| || ||||| |||||||| || |||   
-actgaggaatatattaaag--ctaaccagttatgtatggattgtta-agtttttaattgttgatgctattatttaatcttctctttgcttgtaatgtatgtagGGGCCCTGGTCGTTTTGAAG---ACAGACCAAGGTTTGGAGACAGGGATGAGTACCGTGGTGGCCCTCGTGGTGCTCCCGGTGACTTTGGTGGCGATAAGAGT

upper sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------------aactga-ggcatatctgcatgttctgttgaattct---tgagctactgtggcaatattttctagttgtcgt----ttggctgatttctgattcctgtgatg-tgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG
                                                                                              | | ||  |   | ||   |   |||   |||   ||   | |  ||    | ||||  |||| |  |    |    ||  || || |     |  || | || || || |||||||| || ||||| || |||||||||||||| ||||||||||| |||||||| || || || ||  | || ||||| |||||||   ||   
gtaatgactcaattttgagttgatgttcggtgatttatttatttatttatttatttattattctgttgttaaacaatttggtgcgcattggggttaatggtttgattacaatgtgaattgggatctgtttggattgccatgttt-tgtttttgagttcttatgatgtaaaatgggttttgttgaaaattgtgattttcagTGGTCCACCTCGCTTTGAAGGAGATAGACCAAGGTTTGGTGACCGGGATGGGTACCGTGGAGGTCCACGAGGACCTCCAGGTGAGTTTGGTGACAAGGGT

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|58586656|gb|CF984964.1|CF984964
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|4880983|gb|AU065282.1|AU065282
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|88363743|gb|CI609100.1|CI609100
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGGCCCACCTCGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGG-CCCACCTCGG
EST: gi|86838292|gb|CI327685.1|CI327685
EST:     TCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: TCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|8334614|gb|BE039598.1|BE039598
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|25800452|gb|CA756413.1|CA756413
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|163929239|gb|EG712692.1|EG712692
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|86539940|gb|CI180146.1|CI180146
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCTCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|86539956|gb|CI180162.1|CI180162
EST:     AGGCCACCAGTCCGCCCATTTGGCTCTGGCCCCGCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|11863303|gb|AU065659.2|AU065659
EST:     AGGCCANCAGGCCGCCCATTTGGCTCTGGCCCCC-TGGTGATCGCC-AAG                         GGGCC-ACCTCGGTTCGAAGGG-ACAGAC-AAGGTTTGGAAACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|88987135|gb|CI034176.1|CI034176
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|86429864|gb|CI082287.1|CI082287
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|117232299|gb|CT860043.1|CT860043
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|86871570|gb|CI342369.1|CI342369
EST:     GCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGTTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: GCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|88969558|gb|CI383067.1|CI383067
EST:     CCCTGGTTATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGGACAGACCAAGGTTTGGAGACCGGGATG
genomic: CCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAA-GGGGACAGACCAAGGTTTGGAGACCGGGATG
EST: gi|55413805|gb|CV726181.1|CV726181
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|58665575|gb|CK054261.1|CK054261
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|88426462|gb|CI576704.1|CI576704
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCG
EST: gi|86539973|gb|CI180179.1|CI180179
EST:     AGTCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
EST: gi|88356652|gb|CI617735.1|CI617735
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCATCTCGGTT
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTT
EST: gi|88691924|gb|CI735499.1|CI735499
EST:     AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAG                         GGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG
genomic: AGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGG

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), 71 (downstream exon)
Score: 16

ACCTTAACTTGCCGTCTGAGATTGTACCTGCTACACTCAAGAAGTCTGCAAGGCCACCAGGCCGCCCATTTGGCTCTGGCCCCCCTGGTGATCGCCCAAGgtcctaattt ... atgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaatattttctagttgtcgtttggctgatttctgattcctgtgatgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG
                               ttctgat  putative branch site (score: 16)
     tattttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgaggcatatctgcatgttctgttgaattcttgagctactgtggcaatattttctagttgtcgtttggctgatttctgattcctgtgatgtgtttagGGGCCCACCTCGGTTCGAAGGGGACAGACCAAGGTTTGGAGACCGGGATGGCTACCGTGGTGGACCTCGTGGTGCGCCTGGTGATTTTGGTGGTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- ctgaggc
- - - - - - - tgcatgt
- - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - -gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattc