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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g39570.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
---tgaatgtttagctgaaccacaac-tgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
   ||   ||     |    ||     | | || ||     |  | ||  |||  |  | |||    |||  |||||| | ||    |    |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | |||||||| |||||||||||||||
tgatgccggtaccattttctcatgctgttttatctaactgctccaagct-att--agctgttgcaaaactcttgcataatggagggatcattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccatt-caaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
|||  |     ||        |   |  ||||   |  |  | |        |  |||||    |||  |||||| | |||  |||   |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | || ||||| ||||||||||| |||
tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 10
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattca-aattattgtgggacttctgcatacttgataacttgccgcgattgtg---cagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
  | | ||| |||       || ||||  |  |    | | | |  ||| | |  |  | |   | || || ||  || |  | |||    | || ||   ||||||||||| ||| | |||||||||||||||||||| ||  |||| || || |||||||| ||||||
aaagtattt-gctagttttgaaatgtc--tgccctgatgacttcagattgacagatcctttattatttttg-atttttaactaattggtatgcttttgaaccagCTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 10
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtg---cagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
  | | ||| |||       || ||||  |  |    | | | |  |||   |      |     || |  ||  ||    | |||    |||  ||   ||||||||||| ||| | ||||||||||||||||| || ||  |||| || || |||||||| ||||||
aaagtattt-gctagtttggaaatgtc--tgccatgatgacttcagattggcagatccttcattattttcaatttttatctaattgatatgatcttgaaccagCTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgat--aacttgccg--cgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
  ||    ||  |||| |   |||   |||| |    |||||  | |||    ||  | | |   ||  |  |   || |  || |||  |   |   ||  |||||||||||||||| ||||||||||||||| | |||||| | |||||||| ||||| || ||||||
--aaaaaatatatgaagc-tgacttggattttccatcttaatctctattttt-ttgcttttgtgttttggattttgtgctgaaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG

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|88488548|gb|CI425819.1|CI425819
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTNATCACACTGTTACGTTACAN                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88539198|gb|CI468290.1|CI468290
EST:     ATGTTTCTGATCACAGCTGTTACGTTACAG                         CTTACT-GGGATTCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
genomic: ATGTTTCTGATCACA-CTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGA-TCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
EST: gi|29676546|gb|CB672821.1|CB672821
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88538414|gb|CI467440.1|CI467440
EST:     CACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGNTTGCATTACAAAGGCTNTTGGAGCCT
genomic: CACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88512954|gb|CI440460.1|CI440460
EST:     CTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAANATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: CTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88284518|gb|CI405964.1|CI405964
EST:     TCTTCCGGGCAAAATCTGGTGATGTTTCTGATCACACTNTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|29656805|gb|CB653080.1|CB653080
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88832223|gb|CI017457.1|CI017457
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|15853702|gb|BI806498.1|BI806498
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88478672|gb|CI415943.1|CI415943
EST:     GGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: GGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88906495|gb|CI375567.1|CI375567
EST:     TCTTCCTGGCAAAATCGGTTGATGTTTCTGATCACACTGTTACGTTACAGG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACA-Ggtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
EST: gi|32948291|gb|BP184863.1|BP184863
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88508589|gb|CI436095.1|CI436095
EST:     AATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: AATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|32948361|gb|BP184933.1|BP184933
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCC
EST: gi|86522997|gb|CI163203.1|CI163203
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88481174|gb|CI418445.1|CI418445
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACNTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGGTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|33682201|gb|CF310440.1|CF310440
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88502715|gb|CI430221.1|CI430221
EST:     TGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88552259|gb|CI480930.1|CI480930
EST:     TTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|87021293|gb|CI295352.1|CI295352
EST:     TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: TCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88273463|gb|CI393869.1|CI393869
EST:     CTTCCGGGCGAAATCTGGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
genomic: CTTCCGGGCAAAATCT-GTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT
EST: gi|88513717|gb|CI441223.1|CI441223
EST:     TCTGTTGATGTTTCTGATCACACTGTTACGTTACAG                         CTTACTGGGGATCTCGACAAGATGGTTNCATTACAAAGGCTGTTGGAGCCT
genomic: TCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCT

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), 66 (downstream exon)
Score: 77

GGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTGAAATCTTCCGGGCAAAATCTGTTGATGTTTCTGATCACACTGTTACGTTACAGgtaattttaa ... gattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG
                               tgataac  putative branch site (score: 77)
     aaattattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG