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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaggtcgattttggaaactaaaatacttggaagtacttttctgagtaggacgataaatatactaagtagattctgcttaccttcttctgccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT

Basic information

species Oryza sativa
transcript LOC_Os01g37480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G130101_T01 (Zea mays), 3'ss of exon 1
-----ataag-gtcgattttggaaactaaaatacttggaagtacttttctgagtaggacgataaatatactaagtagattctgcttaccttcttctgccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT
     ||| | ||  |||      | || || | ||||| ||| |||| |||| ||||  |||| | | |||||  ||||  |||| |    ||||| ||||||||||| |||||||||||||||||||||||||| || |||||||| ||||| || |||||||| ||||| ||||||||||||||| |||||||||| ||| | 
tgtgtataggagttaattggaaggattagaagagttgga-gtaattttatgagcaggaacataa-tttgctaaggggatttcgcttgc----ttctggcatttcagGGTTCCTTGTAGAGCAGGCACATGCACAACTCCTATTCAAGTCACATCGTCTCAGTTGGTGTCAAACGAGATATTCCCACCAGCTGTTGTGAAGGCCATG

upper sequence: LOC_Os01g37480.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G070890_T01 (Zea mays), 3'ss of exon 1
-----ataagg-tcgattttggaaactaaaatacttggaagtacttttctgagtaggacgataaatatactaagtagattctgcttaccttcttctgccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT
     ||| |  |  |||      | || || | ||||| || ||||| |||| |||   |||| | | |||||  ||||  |||| |    || || ||||||||||||||||||||||| |||||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||||||| || |||||||||| ||| | 
tgtgtataggaattaattggaaggattagaagagttgga-gttcttttatgagcagggacataa-tgtgctaaggggatttcgcttgc----ttttggcatttcagGGTCCCTTGTAGAGCTGGCACATGCACAACTCCTATTCAAGTAACATCATCTCAGTTGGTCTCAAATGATATATTCCCAGCAGCTGTTGTGAAGGCCATG
















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|88412518|gb|CI688868.1|CI688868
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|41881445|gb|BX927417.1|BX927417
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|86907695|gb|CI296636.1|CI296636
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|42793984|gb|AB117883.1|AB117883
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|33801009|gb|CF326378.1|CF326378
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|88422254|gb|CI689058.1|CI689058
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|88368879|gb|CI651481.1|CI651481
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|86891442|gb|CI308077.1|CI308077
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|88435222|gb|CI581942.1|CI581942
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|428685|gb|D24837.1|D24837
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC
EST: gi|88375428|gb|CI681199.1|CI681199
EST:     GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAG                         GGTCCCTTGTAGAGCAGGCACATGCACAANGCCCATTCAAGTTACATCTTC
genomic: GCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTC

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: 70 (upstream exon), 67 (downstream exon)
Score: 16

GGCGGCCGGTGGGCGGGGGCCGGTGGACGAGCCGCCGGATATCGTTCTACGCCTCCCGCGCCTTCTTCCTCCTCATCATCCTCCAGATCCCGCTCTTCAGgtcgccccct ... gccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaggacgataaatatactaagtagattctgcttaccttcttctgccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT
                              tgcttac  putative branch site (score: 16)
                           ttctgcttaccttctt  CT-rich tract
         ataaatatactaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaggtcgattttggaaactaaaatacttggaagtacttttctgagtaggacgataaatatactaagtagattctgcttaccttcttctgccatttcagGGTCCCTTGTAGAGCAGGCACATGCACAACGCCCATTCAAGTTACATCTTCGCAGTTGGTCTCAAATGAGATATTCCCACCATCTGTTGTGAAAGCCCTT

- - - - - - - - aaactaa
- - - - - - - - - - - - atacttg
- - - - - - - - - - - - - - - - - - - -tttctga