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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatagtataaaacttatattgctgaatatttattgagcagccttacttcttaagccacttcttgctcaataatgtttcccctcctctaatgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGATGCAAATGCACATTTGATCATGAATGGCGAGCTTCGTGCTCTCCAGCCC

Basic information

species Oryza sativa
transcript LOC_Os02g52430.1
intron # 1
splice site 3'
intron type U2

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|88328481|gb|CI676690.1|CI676690
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88336451|gb|CI643264.1|CI643264
EST:     ATCGCCGCCGATCCGACCCCGNGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AAACGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|33687484|gb|CF315723.1|CF315723
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|33687484|gb|CF315723.1|CF315723
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88759865|gb|CI769421.1|CI769421
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88759865|gb|CI769421.1|CI769421
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88762863|gb|CI772419.1|CI772419
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88762863|gb|CI772419.1|CI772419
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88317816|gb|CI672411.1|CI672411
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGNCGCGAGCGAGCAG                       
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGC--G-AGgtaaggaaat ... atgacagc
EST: gi|88744178|gb|CI767538.1|CI767538
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88744178|gb|CI767538.1|CI767538
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88826552|gb|CI777117.1|CI777117
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88826552|gb|CI777117.1|CI777117
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88324924|gb|CI644935.1|CI644935
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88324924|gb|CI644935.1|CI644935
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|55433648|gb|CV729935.1|CV729935
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88826281|gb|CI776846.1|CI776846
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88826281|gb|CI776846.1|CI776846
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88309784|gb|CI656525.1|CI656525
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88695927|gb|CI739502.1|CI739502
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|55413649|gb|CV726025.1|CV726025
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88734915|gb|CI758423.1|CI758423
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88734915|gb|CI758423.1|CI758423
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|33680671|gb|CF308910.1|CF308910
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|33680671|gb|CF308910.1|CF308910
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|58588337|gb|CF986645.1|CF986645
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAAGTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88571530|gb|CI662903.1|CI662903
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|55441666|gb|CV734158.1|CV734158
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88730192|gb|CI753807.1|CI753807
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88730192|gb|CI753807.1|CI753807
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88325993|gb|CI651040.1|CI651040
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGNGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88590627|gb|CI708407.1|CI708407
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88740499|gb|CI764007.1|CI764007
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|88740499|gb|CI764007.1|CI764007
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         C
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcag-
EST: gi|86902092|gb|CI300331.1|CI300331
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
EST: gi|88577614|gb|CI674212.1|CI674212
EST:     ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAG                         AACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA
genomic: ATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGA

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: 75 (upstream exon), 56 (downstream exon)
Score: 3

GAGCCAACCACCACCCCCAATCGGATCCCTCACCCGATTGGCCCGGCCAGATCGCCGCCGATCCGACCCCGCGCAACCCTCTCCCGCGGCCGCGAGCGAGgtaaggaaat ... atgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGATGCAAATGCACATTTGATCATGAATGGCGAGCTTCGTGCTCTCCAGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttcttaagccacttcttgctcaataatgtttcccctcctctaatgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGATGCAAATGCACATTTGATCATGAATGGCGAGCTTCGTGCTCTCCAGCCC
                                        ctctaat  putative branch site (score: 3)
                               tttcccctcctctaat  CT-rich tract
                        aataatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatagtataaaacttatattgctgaatatttattgagcagccttacttcttaagccacttcttgctcaataatgtttcccctcctctaatgacagcagAACCGAATCCAATATGGCTGCCTTGCCATTAGCCACAGCCGAATTATGTGATGCAAATGCACATTTGATCATGAATGGCGAGCTTCGTGCTCTCCAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - gagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgc