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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctcagatgttgccattttataatctattttagggaaaaaaattgtactgacacatactatctaattgttctttgttatttatggcgataatttaagtgaattttttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 4
gtaagttcctcagatgttgccattttataatctattttagggaaaaaaattgtactgacacatactatctaattgttctttgttatttatggcgataatttaagtgaattttttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT
                           |||     |||  |    |   ||||  |      | | |||| || || ||   |              | | ||||||| | || |||||||||||||| || |  ||||||||  |||||  |||||||||||||||||| || ||||||||  ||||||| ||
--------------------------gtaagtc--ttttagatgcaggcttgtg-tagttttttccatctcatggtactccatc-----------cgagtgaagtgaactgttgatttgcagCAATCTGGCAGAAAACCAGTTCTCTGGATCTGTGCCATACTCAATTTCAACGATGCCTAATATTAAGTACCT
















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|88369294|gb|CI577757.1|CI577757
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTG
EST: gi|88311529|gb|CI572585.1|CI572585
EST:     GGTGGGCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88449338|gb|CI582210.1|CI582210
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACC
EST: gi|88385785|gb|CI566647.1|CI566647
EST:     GGTGGCCAAAATATT-AATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|6507597|gb|AU064258.2|AU064258
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88298922|gb|CI567925.1|CI567925
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGC-ATACTCAATTTC-AC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88298740|gb|CI565937.1|CI565937
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTGCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88371283|gb|CI600131.1|CI600131
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTG
EST: gi|88314468|gb|CI604952.1|CI604952
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGACAGGCT                         CAATCTTGCTGGGAAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAAC
EST: gi|88422824|gb|CI573986.1|CI573986
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAAC
EST: gi|88428401|gb|CI564869.1|CI564869
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CACTCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88392563|gb|CI625385.1|CI625385
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAACTCTTGCTGGGAACCAGTTTGCTGGAAATGTGCC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAA-TCTTGCTGGGAACCAGTTTGCTGGAAATGTGCC
EST: gi|88425544|gb|CI569268.1|CI569268
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAAC-AGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88395348|gb|CI611265.1|CI611265
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88385459|gb|CI564119.1|CI564119
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88368294|gb|CI577565.1|CI577565
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATG
EST: gi|88300565|gb|CI587369.1|CI587369
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATANTCAATTT
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTT
EST: gi|88405784|gb|CI609683.1|CI609683
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAG
EST: gi|29631005|gb|CB636014.1|CB636014
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCAC
EST: gi|88430712|gb|CI596826.1|CI596826
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGT
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGT
EST: gi|88412193|gb|CI573469.1|CI573469
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTG
EST: gi|88396144|gb|CI595692.1|CI595692
EST:     GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTG
EST: gi|88314779|gb|CI608238.1|CI608238
EST:     GGTGGC-AAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCT                         CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTG
genomic: GGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTG

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: 67 (upstream exon), 61 (downstream exon)
Score: 25

TGACATGAGCCAAAATAATCTTGGGGGTGGCCAAAATATTCAATACAATCTTCCAAATAAGAAGCTTGAGAGGCTgtaagttcct ... ttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaattgttctttgttatttatggcgataatttaagtgaattttttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT
 atctaat  putative branch site (score: 25)
                                         ttttttattt  putative PPT
                           ataatttaagtgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctcagatgttgccattttataatctattttagggaaaaaaattgtactgacacatactatctaattgttctttgttatttatggcgataatttaagtgaattttttatttgcagCAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA