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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACGGCGAGCGTCCCCGGCGAATCCGCCTTGACGGAGGCACCCCGGCGAGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatccctttgtcccatcacttttcacccgtcaattgcagtccccgacctggtagaggaggggagcacacagccgacgccatagcagcagcaaatc...

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 1
splice site 5'
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|117251528|gb|CT844202.1|CT844202
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|66924263|gb|CX111111.1|CX111111
EST:     AGCTCACCTTCCCGGAGGAATCTCAGCTCAGCCTCGTCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|8857838|gb|AU095156.1|AU095156
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|13422333|gb|AU176452.1|AU176452
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|11565271|gb|AU165907.1|AU165907
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88370619|gb|CI590197.1|CI590197
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88431461|gb|CI579578.1|CI579578
EST:     AGCTCACCTTCCGGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTAAAAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88356835|gb|CI619321.1|CI619321
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCACCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCAATTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88430193|gb|CI565206.1|CI565206
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAAACTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88351304|gb|CI627320.1|CI627320
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58672423|gb|CK061109.1|CK061109
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88425369|gb|CI567089.1|CI567089
EST:     AGCTCACCTTCCCGGAGGAATCCCAGTTCAGCCTCATCGTTTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|33676567|gb|CF304806.1|CF304806
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58674501|gb|CK063188.1|CK063188
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88377696|gb|CI605531.1|CI605531
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58672650|gb|CK061336.1|CK061336
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|2312757|gb|C28912.1|C28912
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58676963|gb|CK065650.1|CK065650
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     AGCTCACCTTCCCGGAGGAATCTCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|58664289|gb|CK052975.1|CK052975
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|33795605|gb|CF323672.1|CF323672
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88414769|gb|CI604127.1|CI604127
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|88368494|gb|CI572703.1|CI572703
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAG                         GGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT
genomic: AGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTT

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: 71 (upstream exon), 49 (downstream exon)
Score: 16

CCAACGGCGAGCGTCCCCGGCGAATCCGCCTTGACGGAGGCACCCCGGCGAGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatcc ... atatctgtagGGAAATATCTTGGTGATTCTTGGGAACCTTCAGAAAGACCACTTAATAGTTTTCCTTGGCCCAGAAAGGCTTGAGGCTTGAGAGCTGAAAAGTTCTGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAACGGCGAGCGTCCCCGGCGAATCCGCCTTGACGGAGGCACCCCGGCGAGCTCACCTTCCCGGAGGAATCCCAGCTCAGCCTCATCGTCTTCGGTGAGgtacgcatccctttgtcccatcacttttcacccgtcaattgcagtccccgacctggtagaggaggggagcacacagccgacgccatagcagcagcaaatc

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgacg