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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagattgttgaattattgatagtatatattttggtgcttcattgaaattaatttagaatactttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG

Basic information

species Oryza sativa
transcript LOC_Os03g03920.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G057158_T02 (Zea mays), 3'ss of exon 6
---tttagattgttgaattattgatagtatatattttggtgcttcattgaaattaatttagaatactttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG
   || |  |  || || | || | |   |  | |    | ||  || ||  |  || |    |   ||| |   || || | |   |  |||| ||| | |||||||   ||||||||||   |||||| ||||||||||||||| |||||||||||||||||||||||||| | ||| || ||||
aacttgacttaatttaactttttagacagttgactgcctttctaaatggatttacatgtgcccttgcttattta-acaaccttttgaa--acttgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG

upper sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 6
tttagattgttgaattattgatagtatatattttggtgcttcattgaaattaatttagaatact-ttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG
 ||    |  | ||   |   |||    |    ||    |  ||  | ||| |  ||      |  |  |   || |||| ||  |  |||| ||| | |||||||   ||||||||||   |||||| ||||||||| ||||| |||||||||||||||||||||||||| | ||| || ||||
cttgatctaattaaacttctttagacagttgactgcctttctatgtagatttacatattcccttgcttgtttaacaacttttggaaa-acttgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG
















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|29672914|gb|CB669189.1|CB669189
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATTTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|88955460|gb|CI091552.1|CI091552
EST:     ACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: ACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|89176589|gb|CI111305.1|CI111305
EST:     CCCAGAGCGAACCCGATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: CCCAGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|88955489|gb|CI091581.1|CI091581
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|88849094|gb|CI087616.1|CI087616
EST:     CTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: CTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|88844161|gb|CI001218.1|CI001218
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|86482742|gb|CI125375.1|CI125375
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|157650080|gb|EX449714.1|EX449714
EST:     GCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: GCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|87020032|gb|CI277764.1|CI277764
EST:     AGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|86500583|gb|CI143216.1|CI143216
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|86429591|gb|CI076272.1|CI076272
EST:     CCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCTACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: CCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|88850993|gb|CI096383.1|CI096383
EST:     GCTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: GCTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|86413823|gb|CI068030.1|CI068030
EST:     GCTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: GCTGGCCCAGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
EST: gi|86486868|gb|CI129501.1|CI129501
EST:     AGAGCGAACCCAATCAGGTGCTGGTGCAG                         GCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG
genomic: AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTG

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: 75 (upstream exon), 75 (downstream exon)
Score: 57

AGAGCGAACCCAATCAGGTGCTGGTGCAGgtaacttcct ... ttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattaatttagaatactttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG
     taatttagaatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagattgttgaattattgatagtatatattttggtgcttcattgaaattaatttagaatactttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - -tgttgaa
- - - - - - - - - - - - - - - - - -gtgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatga