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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtcccagatgaactttaccatttttttctcgaaagcagatgaagtttaccattgctcttatagaattttcttgtcattttaaaaccacttctaagttctctttgcttttgatttgtacag

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G069758_T01 (Zea mays), 5'ss of exon 11
GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtcccagatgaactttaccatttttttctcgaaagcagatgaagtttaccattgctcttatagaattttcttgtcattttaaaaccacttctaagttctctttgcttttgatttgtacag
|| ||||||||||| |||||||| || ||||||||||||||||||||  || |  ||  |  || || |                     |  || |    ||  |||      ||||||||   || ||||||       | | |  |||||||| | ||||  ||||
GGAACTGGAGATTTGACAACTGCTCTCCTACTAGGATGGAGTAATgtgagtactggagaacattcacta---------------------acattca----tgtccttg----gttttcttgc--ttctaaaac-------atggttgctttgcttgtaatttacacag
















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|427643|gb|D23776.1|D23776
EST:     GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGNGTAAT                         AAATACCCTGNTAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88527260|gb|CI455400.1|CI455400
EST:     TTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: TTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88266886|gb|CI368662.1|CI368662
EST:     TCACGGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: TCACGGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|86885325|gb|CI317085.1|CI317085
EST:     GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|13165352|gb|AU174149.1|AU174149
EST:     GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88540839|gb|CI468912.1|CI468912
EST:     CGGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: CGGGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|89185094|gb|CI049640.1|CI049640
EST:     GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88227203|gb|CI228316.1|CI228316
EST:     CCTTCTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: CCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88473155|gb|CI410426.1|CI410426
EST:     GGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
EST: gi|88543303|gb|CI473300.1|CI473300
EST:     GGCACTGGAGATTTAACAACTGCCCTTTTACTAGGATGGAGTAAT                         AAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG
genomic: GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTG

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: 45 (upstream exon), 54 (downstream exon)
Score: 20

GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtccca ... atttgtacagAAATACCCTGATAACCTTGAGAGGGCGGCTGAACTGGCGGTATCCAGTTTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACTGGAGATTTAACAACTGCCCTTCTACTAGGATGGAGTAATgtaggtcccagatgaactttaccatttttttctcgaaagcagatgaagtttaccattgctcttatagaattttcttgtcattttaaaaccacttctaagttctctttgcttttgatttgtacag

- -  TGGAGA
- - - GGAGAT
- - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - GATGGA