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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatattagtctgtttgttttcttaattttcattaactcctgccagttacaagcaatagaagttcctagcattgtctgaatattaccgtatgatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g37870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 5
gtaatatattagtctgtttgttttcttaa--ttttcattaactcctgccagttacaagcaatagaagttcctagcat--tgtctgaatattaccgtat------gatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG
|| || |||   ||  |||||    || |  ||||  ||   |   |    ||        |      | | | |||  ||||| |  |  |  | ||       | | | |||| |||||||| |||||||||||||||||||| || ||||||||||| |||||||| || ||||||||| |||||
gtgatctatctctccatttgtcagattgaatttttgtttggattaggttcatttttgtgtgtgcgcaatgcaaacatcatgtcttagcaccattgaattttagaaacctaatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG

upper sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 5
gtaatatattagtctgtttgttttcttaattttcatt--aact---cctgccagttacaagcaata-gaagttc-----ctagcattgtctgaatattaccgtatgatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG
|| || |||    |  |||      | |||||| |||   | |           ||    |||||   ||||||      |||||   | ||||| |||       |   | |||| ||||||||||||||||||||||||||||| || ||||||||||| ||| |||| || ||||||||| |||||
gtgatctatctcccatttttcagaatgaatttttatttggattaggttcattttttttgtgcaatgcaaagttcatgtcttagcaccatttgaattttagaaaccaacttattttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG
















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|88850020|gb|CI091315.1|CI091315
EST:     TGTTTGTCTTCTCNATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|87013802|gb|CI269301.1|CI269301
EST:     TCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88903030|gb|CI088568.1|CI088568
EST:     TGTTGGTCTTCTCGATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88241455|gb|CI241304.1|CI241304
EST:     TG-TTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86545913|gb|CI186119.1|CI186119
EST:     TCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|89180088|gb|CI044367.1|CI044367
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86828209|gb|CI276815.1|CI276815
EST:     GGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88849106|gb|CI087628.1|CI087628
EST:     G-TTGNTCTTCTCNATCGTTGGTGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: GTTTG-TCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88239196|gb|CI240358.1|CI240358
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|66915129|gb|CX101977.1|CX101977
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGATATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGTTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|25806580|gb|CA762541.1|CA762541
EST:     TGTTTGTCTTCTCNATCGTTGATGACCATGTTTGGTTTAGGAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88202662|gb|CI201017.1|CI201017
EST:     GTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: GTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86431994|gb|CI085605.1|CI085605
EST:     TGTTNGTCTTCTCNATCGTTGGTGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86855222|gb|CI265148.1|CI265148
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|27577569|gb|CB000264.1|CB000264
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86412482|gb|CI017350.1|CI017350
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|87036060|gb|CI189507.1|CI189507
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|88981009|gb|CI021136.1|CI021136
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
EST: gi|86545709|gb|CI185915.1|CI185915
EST:     TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAG                         ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC
genomic: TGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGAC

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: 50 (upstream exon), 74 (downstream exon)
Score: 23

ATTTGCTACTCCAAAAGATCATCGAAAGGCAAAGCCTTTTCATGACCATGTGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATCAGgtaatatatt ... actttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaatagaagttcctagcattgtctgaatattaccgtatgatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG
                                              ctttgtc  CT-rich tract
                         tgaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatattagtctgtttgttttcttaattttcattaactcctgccagttacaagcaatagaagttcctagcattgtctgaatattaccgtatgatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG