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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattctaccatcgttgttagatgttctctttctttctttctttctttctttctttttttttttggcattcatggacctttattttattttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCA

Basic information

species Oryza sativa
transcript LOC_Os10g36760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 1
tgcattctaccatcgttgttagatgttctctttctttctttctttctttctttctttttttttttggcattcatgg---acctttattttattttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCA
   ||| |    ||  || ||  | | |||                |||  |||  | | | | ||| ||  | |    |  | |||  | |||   ||||||||||||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||| || || || ||| |||| ||||||||||||||| ||||||
--tatttttatctcagtggtat-tatgctccagaagaaaacaaagatttagttcactgtatctatggtatggacgaggaatttatatgctttttcatatgcagGACCATCGGCAATTCAAACAGCGGTACTACGAATTTCTCGACTACTACCGAGCTCCAAATGGCCCGATCTTCCTATACATCTGTGGAGAATCTACGTGCA
















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|29667887|gb|CB664162.1|CB664162
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88732121|gb|CI757298.1|CI757298
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88738898|gb|CI762406.1|CI762406
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88731615|gb|CI755228.1|CI755228
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|29635606|gb|CB640615.1|CB640615
EST:     CGCAGGAGGAGCGGTGGATGGACCANACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88402336|gb|CI596197.1|CI596197
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTAGTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88312989|gb|CI592273.1|CI592273
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|33797174|gb|CF324451.1|CF324451
EST:     CTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88720865|gb|CI744164.1|CI744164
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGNAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|29678499|gb|CB674774.1|CB674774
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88315058|gb|CI610117.1|CI610117
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|88745280|gb|CI768640.1|CI768640
EST:     CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: CGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
EST: gi|33794179|gb|CF322980.1|CF322980
EST:     GGACCAGACCCTCGACCACTTCAACCCCACC                         GACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA
genomic: GGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGA

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: 63 (upstream exon), 75 (downstream exon)
Score: 16

CGGTGGCGGGGGGCGCCTCGGCGGCGCCGCCGCACCAGGCAGGTACCTGACGCAGGAGGAGCGGTGGATGGACCAGACCCTCGACCACTTCAACCCCACCgttgagtccc ... ttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctttctttttttttttggcattcatggacctttattttattttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCA
                                cctttattttattttc  CT-rich tract
                                  tttattttattttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattctaccatcgttgttagatgttctctttctttctttctttctttctttctttttttttttggcattcatggacctttattttattttcaatgcagGACCATCGGCAATTCAAGCAGCGTTACTATGAATTCCTTGATTACTACCGAGCTCCAAAAGGGCCAATTTTCTTATATATCTGTGGAGAATCTTCGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
tgcattc
- - - - - - - gttgtta