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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG

Basic information

species Oryza sativa
transcript LOC_Os05g49300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G141252_T01 (Zea mays), 3'ss of exon 2
-----cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagt-tctat-tgacttatcat-gtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
      ||  ||||    ||  |   | | ||  |  ||||| | |        |  || |||| || ||  |  | | ||   | |||  ||| ||| | ||| ||| ||||| |||||||| || || ||||| || || ||||| |||||||||||||| || ||||| |||||||||||||||||||||||||| || || |||
gtaagtttcgaatcggcctggatatggtc-gtcccatgcattccatatttcttggggttgttgtactgatacgtctatatacacgcctttccattgtcttttttgcagCGAGATTGCGAAGCACCTGTCTCTTCCACCAGTGAAGCTGCACTGCAGCATGCTCGCTGAGGACGCAATCAAGGCCGCCGTGAAGGATTACGAGGCAAAG

upper sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0127g00460.t01 (Vitis vinifera), 3'ss of exon 1
--cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
  ||| || |  |||| | |   |  ||   ||    |  |   |     |  |||| | |     ||   |||||  ||  |     ||       |  || ||||| || || ||||| || ||||| || || ||||| ||||||||||||||||| ||||||||||| ||||| || || || ||||||||||| |||
aacttgca-ttatattttttattgt-tgctactgatttctcgaagtttttatttttaatttttgtctttttgttctgatgtgtatatttgatgacaatgaagGGAGATTGCCAAACATCTCTCTCTTCCTCCAGTGAAGCTGCACTGCAGCATGCTTGCTGAGGATGCAATTAAGGCAGCTGTCAAAGATTATGAAGCCAAG

upper sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
cttacaatcctattgtcttccgcc-tgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
  |    |   || |  | ||||  |||| ||          |  || | |  ||  |  |   ||  |     |  ||        ||  || | | |||||| || || ||||| ||||| || || ||||| ||| | ||||||||||||||||| || ||||| ||||| || || |||||||| ||  |  | |||
-attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

upper sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
                              || | || |||    | | | |||        |   |  | |    |  ||  || | || | ||  |||||| || || |||||||| ||||| ||||| || ||||||||||||||||||||||| |||||||| ||||| |||||  | || ||||| || ||||||
-----------------------------gtaacttttcttcttgagaggattt--------ctccgaggctaagctctctcctctt-tcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

upper sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
                              ||   || |||    | | | ||| |          |  | |    | | |  || | || | ||  |||||| || || |||||||| ||||| ||||| || ||||||||||||||||||||||| |||||||| ||||| |||||  | || ||||| || || |||
-----------------------------gtaatttttcttcttgagaggatttttc--------cgaggctaagctcattcctctt-tcttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG

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|218490815|gb|FG953065.1|FG953065
EST:     GGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: GGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|11025022|gb|AT003404.1|AT003404
EST:     TCAATCAAGACCAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: TCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|218487080|gb|FG950376.1|FG950376
EST:     GAGTGGGTGAAGGGAATACAAATGGAGGATGCAGCTTCAATCAAGAACAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|218497609|gb|FG955189.1|FG955189
EST:     GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|218501867|gb|FG958628.1|FG958628
EST:     GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCACGAACAG                         TGAGATAGCGACGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|15846947|gb|BI795223.1|BI795223
EST:     AATGGAGGATGCAGCTTCAATCAAGAACAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: AATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
EST: gi|218488996|gb|FG952433.1|FG952433
EST:     GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAG                         TGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT
genomic: GAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCAT

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: 55 (upstream exon), 73 (downstream exon)
Score: 9

CCAGTGAGTGGGTGAAGGGAAAACAAATGGAGGATGCAGCTTCAATCAAGAACAGgtaaataact ... ctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG
                            tattgac  putative branch site (score: 9)
                                           tcctgttttc  putative PPT
      tttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttacaatcctattgtcttccgcctgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - -ccgcctg
- - - - - - - - - - - - - - gctagca
- - - - - - - - - - - - - - - - - -ttgcttg
- - - - - - - - - - - - - - - - - - - - - -gcacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgt