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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatcttatcgtgttcattttatgtaattaagtgcatgttatgcagccattgaaaccgaggtcatccttctcaatataatcctgtattttgttctatgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTAC

Basic information

species Oryza sativa
transcript LOC_Os10g28350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S69_28V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gttcgtatcttatcgtgttc---attttatgtaattaagtgcatgttatgcagccattg-aaaccgaggtc-atccttctca-----atataatcctgtatt-------ttgttcta--tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTAC
       || ||  | | ||| ||    | ||||| |    ||       ||||||  |  |      |   | || || ||||  |     | | |  | || |||       ||| |  |  |||| |  ||| ||||||||| |  | |||| | | || |  |||||||| |||    ||||||| |||| |||||||||  ||||||||||||  ||||||||||||||
gtaagcatcttaaatcaacgtctttgctactttatttgcacaa-catgccttatgcgactctgatgggctaggatcgattcttcctacataaacacacacttgcattgcagttgttgatgcagttgttttacagGTTACTTTGATATTCGCGACCCAGAAGACCGTTGGATTCGAATATGGGTGAAGAAGGGAGACATGATTGTGTTGCCTGCAGGGAGTTACCACCGCTTTAC
















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|33682515|gb|CF310754.1|CF310754
EST:     AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATATCACTGA
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|33693837|gb|CF322076.1|CF322076
EST:     TGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
genomic: TGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|88316332|gb|CI621571.1|CI621571
EST:     AGAACACCTGCATAC-GATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTG
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTG
EST: gi|9865230|gb|AU100980.1|AU100980
EST:     AGAACACNTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGAAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|33682516|gb|CF310755.1|CF310755
EST:     GCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATTGATCAGTGGATTCGTATATCACTG
genomic: GCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAA-TGATCAGTGGATTCGTATAGCACTG
EST: gi|88275016|gb|CI395620.1|CI395620
EST:     ACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCCAAATGATCAGTGGATTCGTATAGCACTGA
genomic: ACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|313081104|gb|HO213690.1|HO213690
EST:     AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|33693836|gb|CF322075.1|CF322075
EST:     AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA
EST: gi|88335605|gb|CI642829.1|CI642829
EST:     AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGT
genomic: AGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGT
EST: gi|88992645|gb|CI035679.1|CI035679
EST:     CCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTG                         GATACTTTGATGTGAGAGACCCAAATGATCAGTGGATTCGTATAGCACTGA
genomic: CCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGA

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), 61 (downstream exon)
Score: 15

TGCCCAGAGAAGCTGCCAAATTATGAAACTAAGATCAAGAGTTTCTTTGAAGAACACCTGCATACCGATGAAGAAATACGCTATTGTCTTGAAGGGAGTGgttcgtatct ... tgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaccgaggtcatccttctcaatataatcctgtattttgttctatgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTAC
                   tcaatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatcttatcgtgttcattttatgtaattaagtgcatgttatgcagccattgaaaccgaggtcatccttctcaatataatcctgtattttgttctatgttgttaagGATACTTTGATGTGAGAGACCAAAATGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG