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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTCGGGGAGGAAGTCAAATTCAATGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaaaatacaaagcattcagtttcttttcttttcctcctggcatcgtgatataacatgttattatcagtaaatatgttcatcattttgcatcat...

Basic information

species Oryza sativa
transcript LOC_Os05g29860.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29860.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 4
GCTGCTCGGGGAGGAAGTCAAATTCAATGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaaaatacaaagcattcagtttcttttcttttcctcctggcatcgtgata-taacatgttattatcagtaaatatgttcatcattttgcatcat
|| ||||| || ||||| |  ||| |||||||||| |||||||||||||||||||||||| |  |||| || || |||| ||||||  ||         |||   |   | |  |  | | ||   || | | |    || | | ||| ||     |   |  | | |   |  ||| 
GCCGCTCGAGGTGGAAGCCGGATTGAATGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacacgatgtctcttcatcatactgcgtacagtgac-cttgctttcctaagagctgcaagatgttagcatattgtgcctcaaccttaaagtgtcac
















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|29675291|gb|CB671566.1|CB671566
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88667078|gb|CI719214.1|CI719214
EST:     TGGAAAGGATTGTATTCTGGATTACCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|87017421|gb|CI287961.1|CI287961
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88905625|gb|CI712924.1|CI712924
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTAC
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTAC
EST: gi|87011172|gb|CI287849.1|CI287849
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTA
EST: gi|88594406|gb|CI714364.1|CI714364
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGA
EST: gi|33682562|gb|CF310801.1|CF310801
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88594629|gb|CI714587.1|CI714587
EST:     TGGAAAGGATTGTATTCTGGATTACCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAA
EST: gi|88905107|gb|CI712406.1|CI712406
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAA
EST: gi|88973494|gb|CI717922.1|CI717922
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTT
EST: gi|33686568|gb|CF314807.1|CF314807
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88675096|gb|CI729209.1|CI729209
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAA
EST: gi|88904956|gb|CI712255.1|CI712255
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTA
EST: gi|88738022|gb|CI761530.1|CI761530
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88676991|gb|CI731104.1|CI731104
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88908777|gb|CI714919.1|CI714919
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCG
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCG
EST: gi|88667588|gb|CI722327.1|CI722327
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88431710|gb|CI576901.1|CI576901
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|11565230|gb|AU165866.1|AU165866
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88669978|gb|CI724094.1|CI724094
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88954949|gb|CI720300.1|CI720300
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATAC
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATAC
EST: gi|88904545|gb|CI711844.1|CI711844
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|2427972|gb|C72435.1|C72435
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88594346|gb|CI714304.1|CI714304
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACG
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACG
EST: gi|88667495|gb|CI722234.1|CI722234
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAA
EST: gi|88959424|gb|CI716793.1|CI716793
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTAT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTAT
EST: gi|88674644|gb|CI728757.1|CI728757
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAA
EST: gi|88673162|gb|CI727276.1|CI727276
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88417331|gb|CI578992.1|CI578992
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAAGTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|33681239|gb|CF309478.1|CF309478
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT
EST: gi|88693111|gb|CI736686.1|CI736686
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATNGCTGGTGTCCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATAAGAACCGACAA
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAA
EST: gi|88595180|gb|CI715336.1|CI715336
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGG
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGG
EST: gi|88410825|gb|CI578631.1|CI578631
EST:     TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCC                         GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTAAT
genomic: TGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACT

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: 52 (upstream exon), 61 (downstream exon)
Score: 8

GCTGCTCGGGGAGGAAGTCAAATTCAATGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaa ... ttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACTGGAGACTTTTCCTGAAAATTTGAGTGCTGTTGCCCATTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTCGGGGAGGAAGTCAAATTCAATGGAAAGGATTGTATTCTGGATTAGCTGGAAATATTGCTGGTGTTCTCCCgtaagtacaaaatacaaagcattcagtttcttttcttttcctcctggcatcgtgatataacatgttattatcagtaaatatgttcatcattttgcatcat

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc