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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggc-atggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT
   ||  | | |    ||   |  |  | || |    || ||||||||   ||  |||    |||||||||| || |||| ||||||   | ||  | |||||||| || ||||| || || || || |||||||||||||||||||| |||||||||||||||| |||||| |||| |||||| |||||  |||| ||||
---gtactgtcgccccagc--gctagctagattca--gcattgagctcacctgttgtgtttgtggttactgactgttgcttctttgcacctcca--tccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
------ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT--
         |||  |||| |  ||  | |  |   ||    || || | |    | ||       ||  |  |     || |||     || ||||   | |||||||  | || |||||||| ||||| || || ||||||||||| ||||| || ||||| ||||||||||| |||||    || ||    |||| |||  | |  
ggtcacaacgtgtcatagctctagcaattgtagatga----ttccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttc--attgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAAAAA---CAAAAGAACTGTGTCATACTCTGA

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 6
-ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT--
  | ||  | |     || ||||| ||     ||| ||||     |||   |||        | |||    |   || |     |  |||||   || |||||  | |||||||| || ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| |||   || || |  ||| | ||  | |  
gtccgtcttgtgac--aaaggagtgaag----ctttttgc----tgctgtgttgt-------ttgttctaaacctcttccaaaat-tctttgtg-ctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAG

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ16760 (Selaginella moellendorffii), 3'ss of exon 6
-ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT---
  | ||  | |     || ||||| ||     ||| ||||     |||   |||        | |||    |   || |     |  |||||   || |||||  | |||||||| || ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| |||   || || |  ||| | ||  | |   
gtccgtcttgtgac--aaaggagtgaag----ctttttgc----tgctgtgttgt-------ttgttctaaacctcttccaaaat-tctttgtg-ctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAGA

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|163920266|gb|EG714451.1|EG714451
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88269641|gb|CI380939.1|CI380939
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|163918056|gb|EG713984.1|EG713984
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88279468|gb|CI400468.1|CI400468
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCCA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCC
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|86861523|gb|CI328204.1|CI328204
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|163928416|gb|EG715420.1|EG715420
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCA
EST: gi|11233553|gb|AU164965.1|AU164965
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|86869483|gb|CI346343.1|CI346343
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|163929342|gb|EG713767.1|EG713767
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88834954|gb|CI370257.1|CI370257
EST:     AACTCATT-GTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAA                         AACATCAAGGCAAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTC
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGC-AAgtactacatt ... gcaactgcagAACATCAAGGC-AGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTC
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|86599058|gb|CI355675.1|CI355675
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|2431385|gb|C73805.1|C73805
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88375099|gb|CI523364.1|CI523364
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88251317|gb|CI349745.1|CI349745
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATC-AGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|33802329|gb|CF327038.1|CF327038
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88260942|gb|CI364518.1|CI364518
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|88322185|gb|CI537768.1|CI537768
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|86598350|gb|CI354967.1|CI354967
EST:     AACTCATT-GTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         AACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA                         A-CATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA
genomic: AACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCA

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: 66 (upstream exon), 73 (downstream exon)
Score: 46

GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAAgtactacatt ... gcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT
                    tactgat  putative branch site (score: 46)
                                        cctttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggcatggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - agtaaaa
- - - - - - - - - - - - - - - - ttgttgc
- - - - - - - - - - - - - - - - - - - - - - gctccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct