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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtactgcttcagtaaaagtcttattgaacttgagctagatatgtgataaatcatctttagttatttgtgttgtttccctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g02350.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 6
----tgagtactgcttcagtaaaagtcttattgaact--tgagctagatatgtgataaatcatcttta-gttatttgtgttgtttcc-ctgactccc--tgcattca----cagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
    | | | | || |   |     |   | ||||||  | |||||| |||||     |   |    | || || |   |||      |||| |     | ||| |     |||||||||||||||||  | ||||||   || |||||||||||| | |||||||||||||| |||||||||||||||||||||||
gttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 5
tgagtactgcttcagtaaaagtcttattgaacttgagctagatatgtgataaatcatctttagttatttgtgttgtttcc--ctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
 |    || | |  |      |  ||  |  | |||  | || |     || |||   |  |    | | ||||  ||    ||   ||| |  |||  ||||||||||| |||||  | ||||||   || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||
-gttggctacatatgctgttattataccgtgcatgacgt-gagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG
















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|58686212|gb|CK074899.1|CK074899
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29616864|gb|CB621876.1|CB621876
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|58691077|gb|CK079764.1|CK079764
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29663346|gb|CB659621.1|CB659621
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTTAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATA
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATA
EST: gi|58679114|gb|CK067801.1|CK067801
EST:     TGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: TGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|58598121|gb|CK008649.1|CK008649
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29657466|gb|CB653741.1|CB653741
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29662231|gb|CB658506.1|CB658506
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|27577759|gb|CB000454.1|CB000454
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29663347|gb|CB659622.1|CB659622
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29661178|gb|CB657453.1|CB657453
EST:     CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
EST: gi|29619982|gb|CB624994.1|CB624994
EST:     CANNNNNNNATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG                         GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG
genomic: CATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAG

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: 69 (upstream exon), 65 (downstream exon)
Score: 44

ATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAGgtgatttctc ... gcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgataaatcatctttagttatttgtgttgtttccctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
                                 ccctgac  putative branch site (score: 44)
                                       ctccctgc  CT-rich tract
          atctttagttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtactgcttcagtaaaagtcttattgaacttgagctagatatgtgataaatcatctttagttatttgtgttgtttccctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - ctgcttc
- - - - - - -agtaaaa
- - - - - - - - - - - - - - - - - - - - - - tgtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg