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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaataacccatgcaccatgttaatttacctgtgaaactatcaaggtaatactactaaacatcagtctatttactgctatgcattttggcatttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCTCCCTGCAGTGCCGGCGCACGAAGCCGGCGTCCCTCCACCGGAGTCGGCC

Basic information

species Oryza sativa
transcript LOC_Os01g71190.1
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|88368758|gb|CI648357.1|CI648357
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38480813|gb|CF964902.1|CF964902
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38472392|gb|CF956523.1|CF956523
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38468930|gb|CF953061.1|CF953061
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38478017|gb|CF962150.1|CF962150
EST:     CGTCGCGTGGGCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|33662243|gb|CF293210.1|CF293210
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCATGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38478437|gb|CF962570.1|CF962570
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88340238|gb|CI652587.1|CI652587
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|38476080|gb|CF960213.1|CF960213
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88308500|gb|CI650909.1|CI650909
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88361048|gb|CI646072.1|CI646072
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88309673|gb|CI656414.1|CI656414
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88581987|gb|CI699207.1|CI699207
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCGCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88302669|gb|CI668515.1|CI668515
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88903811|gb|CI711513.1|CI711513
EST:     GTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTC
genomic: GTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATG-CCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTC
EST: gi|38469386|gb|CF953517.1|CF953517
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88375345|gb|CI681110.1|CI681110
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCGCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88382283|gb|CI633141.1|CI633141
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88727488|gb|CI751143.1|CI751143
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88330788|gb|CI636797.1|CI636797
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88310290|gb|CI659080.1|CI659080
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
EST: gi|88333512|gb|CI656584.1|CI656584
EST:     CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAG                         GTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT
genomic: CGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCT

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), 71 (downstream exon)
Score: 7

CAAGAGCCACCAAACGGCAGCAGGATGGCCGCTGTGATGAAAGCTCTCGCCGTCGCCTCGCCGATCTCGGCACGAGCACAGCCCCGACGATGCCCCGCAGgtatggctct ... catttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCTCCCTGCAGTGCCGGCGCACGAAGCCGGCGTCCCTCCACCGGAGTCGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaatactactaaacatcagtctatttactgctatgcattttggcatttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCTCCCTGCAGTGCCGGCGCACGAAGCCGGCGTCCCTCCACCGGAGTCGGCC
        tactaaa  putative branch site (score: 7)
                                             catttttc  putative PPT
                     tctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaataacccatgcaccatgttaatttacctgtgaaactatcaaggtaatactactaaacatcagtctatttactgctatgcattttggcatttttcagGTTCGTCAGGCGGCCCTAGCCAAAGCCTGCATTCATCGTTCGGCGGCGTCTCCCTGCAGTGCCGGCGCACGAAGCCGGCGTCCCTCCACCGGAGTCGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
-aaaataa
- - - - -ccatgca
- - - - - - - - -catgtta
- - - - - - - - - - - - - - -cctgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgca