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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttcttacatcttctgtccattcctcgtccaatgtaatctctttgcagttattagccctgagaaatcataacactggaagtttggtttcacagat...

Basic information

species Oryza sativa
transcript LOC_Os02g52650.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G103101_T02 (Zea mays), 5'ss of exon 2
TCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttcttacatcttctgtccattcctcgtccaatgtaatctctttgcagttattagccctgagaaatcat---aacactggaagtttggtttcacagat------------------------
 ||||| ||||| || | |  |||||| ||||| ||||| ||||| || |||||||||||||| || ||||||||||| || |||||||||   ||||| ||||| ||  | ||||  |      | |||| ||   | | |   | |   |   ||  ||  | |  ||| ||    | |   ||||  ||   | ||   |                        
CCTCGGCGAGGAGCCCGAAGCCTTGAAGTGGTACGTTCAGGCCGAGCTCGTGCACTGCCGGTTCGCCATGGCAGGGGTCGCCGGCATCCTTTTCACTGACgtaagcttgct-catccac-----gtccctcttctgtttttacgccctgctaaccatgggctttaatgaatgatctggagagaagaaggctgacctaacccttgctttgcttcgtggctcttcgcag
















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|88311190|gb|CI570264.1|CI570264
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
EST: gi|88302173|gb|CI668019.1|CI668019
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTG
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTG
EST: gi|38475135|gb|CF959268.1|CF959268
EST:     AGGGG-TGCTGGCATCCTTGCGACTGAT                         TTTATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: AGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
EST: gi|33673864|gb|CF302103.1|CF302103
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
EST: gi|88347524|gb|CI637464.1|CI637464
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAAT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAAT
EST: gi|33683439|gb|CF311678.1|CF311678
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
EST: gi|88341656|gb|CI641408.1|CI641408
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAG
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAG
EST: gi|58590186|gb|CF988494.1|CF988494
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTTATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
EST: gi|88288599|gb|CI663388.1|CI663388
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAG
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAG
EST: gi|88571596|gb|CI662969.1|CI662969
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAG
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAG
EST: gi|88332746|gb|CI660264.1|CI660264
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGT
EST: gi|86521070|gb|CI161276.1|CI161276
EST:     TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGAT                         TTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT
genomic: TGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGT

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: 69 (upstream exon), 72 (downstream exon)
Score: 26

TCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttct ... ttctctgcagTTGATACGTGTATCAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGTGCAACAAAATTCGACTTCGCTAACACCACGGCACTCTTCTTTGTCCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCGATGGCAGGGGTTGCTGGCATCCTTGCGACTGATgtaagtttcttacatcttctgtccattcctcgtccaatgtaatctctttgcagttattagccctgagaaatcataacactggaagtttggtttcacagat

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