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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgttgcatcttgggagcaatgacgatcaaattaggttaatgatactcttaacctgcaaattttcctttgaatttataacaagaaatttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143651_T01 (Zea mays), 3'ss of exon 2
tgtttgttgcatcttgggagcaatgacgatcaaattaggttaatgatactcttaacctgcaaattttcctttgaatttataacaagaaattt----cgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG
   |   |||||      |  ||       ||      ||| ||  |  ||||||||     |  || | |||  |||||||  || | |||    | | | ||||||||  |||| |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||
--atatctgcatgcaaacactaaacgtttccagtcatagtttatagttgtcttaacc-atgtaccttgccttgg-tttataatgagcattttttcccttaatagTGGAATTGTAGCCACGGTGTTTGGAGCTACTGGGTTTCTTGGGCGCTATCTTGTGCAACAACTTG
















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|58603608|gb|CK014136.1|CK014136
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88385402|gb|CI630503.1|CI630503
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88356997|gb|CI620885.1|CI620885
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACC
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGC-TACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACC
EST: gi|88383864|gb|CI631754.1|CI631754
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATNATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88388115|gb|CI590391.1|CI590391
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|38565625|gb|CK085078.1|CK085078
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGGCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|29673108|gb|CB669383.1|CB669383
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|86904270|gb|CI306688.1|CI306688
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCG
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCG
EST: gi|29671358|gb|CB667633.1|CB667633
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88443613|gb|CI591838.1|CI591838
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|58663529|gb|CK052215.1|CK052215
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88377002|gb|CI597786.1|CI597786
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88726504|gb|CI750159.1|CI750159
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88447774|gb|CI576970.1|CI576970
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88362216|gb|CI608607.1|CI608607
EST:     GGGACGGGGCATCTCGTCCGGAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATACCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88405560|gb|CI588766.1|CI588766
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88693529|gb|CI737104.1|CI737104
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88362596|gb|CI607354.1|CI607354
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAAC-GGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACG-TGTTTGGAGCTACTGGATTTCTTGGCCGCTAACT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88348839|gb|CI631926.1|CI631926
EST:     GGGACGGGGCATCTCGTCAGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88387570|gb|CI585273.1|CI585273
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88721928|gb|CI743440.1|CI743440
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|58678182|gb|CK066869.1|CK066869
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|2427794|gb|C72257.1|C72257
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTNGAGCTACTTGATTTCTTGGCCGTTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|6012900|gb|AU078717.1|AU078717
EST:     GGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTANCT
genomic: GGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGA-GGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88449234|gb|CI579918.1|CI579918
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88730270|gb|CI753884.1|CI753884
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|33657303|gb|CF279917.1|CF279917
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|58652884|gb|CK041564.1|CK041564
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88356495|gb|CI626110.1|CI626110
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
EST: gi|88358531|gb|CI617617.1|CI617617
EST:     GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAG                         TGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT
genomic: GGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCT

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), 65 (downstream exon)
Score: 38

GTGGAGCGGATGGCGCGAGGTACATGTCCGCGAGGGCGCCGGCGGTCAAGGGGACGGGGCATCTCGTCCGCAAGGGAACCGGAGGGAGGTCGTCTGTGAGgtgaggagct ... ttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactcttaacctgcaaattttcctttgaatttataacaagaaatttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG
                               ttataac  putative branch site (score: 38)
                        tttgaatttataacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgttgcatcttgggagcaatgacgatcaaattaggttaatgatactcttaacctgcaaattttcctttgaatttataacaagaaatttcgtgacagTGGAATCATAGCTACGGTGTTTGGAGCTACTGGATTTCTTGGCCGCTACCTTGTCCAACAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- -ttgttgc
- - - - - - - - - - - - - -gatcaaa
- - - - - - - - - - - - - - - - - - - - - -tgatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - acctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaaa