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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatattttaaaaaatttcatgactgtatgcattttcatatgtaaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC

Basic information

species Oryza sativa
transcript LOC_Os06g43140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
agaaatattttaaaaaatttcatgactgtatgc-attttcatatgtaaggattaaaaattggtcgtaggtt----ccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC
     |  || |     ||   |    || | | | |||  || | |  ||  |   ||    | |   ||    | ||||  ||| |||  |||    ||||||| || || ||||||||||||||||| ||||| || |||||||||||| |||||| 
-----ttattcatggcgttgtttataggtttcctacttttgtaggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT

upper sequence: LOC_Os06g43140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G17340.2 (Glycine max), 3'ss of exon 2
----agaaatattttaaaaaatttcatgactgtatgcattttcatatgtaaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC
     |   |   ||  | | | |    |   | |  | | || |   |  | ||| |  |   | |  || |    | |||  ||    |||  | ||| |||||||||| |||||||| |||||||||||||||||||||||||||||||| || | 
caactgtgttggcttgtacattcttgcaaaaatgtcaactatcttggatttg-attgatgacatgcc--agctcatttaatttctacatatgta-taatttcagGGCCAGATGACATGCCGGCACATATTAAATCGTCGATGTTTGGTTGTGCACTCAT

upper sequence: LOC_Os06g43140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
-------agaaatattttaaaaaatttcatgactgtatgcattttcatatgtaaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC
       ||   |   |||  || | | ||| |||     |   |  ||  |    |||| ||  |     |   ||  || |||   | | |   | |   |||||||||||| ||||||||||| ||||||||||| ||||||||||||||| | || ||
ataagtcagttgttacttattaagtgtaatg-ctgctgttaggctgttagttttccattataatatacatat---ttttctgatttggatttgaaattt---tgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC

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|88323371|gb|CI553616.1|CI553616
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|38480833|gb|CF964922.1|CF964922
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88214425|gb|CI214274.1|CI214274
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88962751|gb|CI023851.1|CI023851
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88209727|gb|CI209576.1|CI209576
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88214454|gb|CI214303.1|CI214303
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|86530349|gb|CI170555.1|CI170555
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88489362|gb|CI426634.1|CI426634
EST:     GGTCCATCTGGTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88691507|gb|CI733585.1|CI733585
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|86417278|gb|CI031487.1|CI031487
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|86511784|gb|CI154417.1|CI154417
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGATGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88503328|gb|CI430834.1|CI430834
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGAGGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88465002|gb|CI514774.1|CI514774
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|86523980|gb|CI164186.1|CI164186
EST:     GAGGGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GTCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GAGGGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
EST: gi|88475322|gb|CI412593.1|CI412593
EST:     GGTCCATCTGCTCCATGGAGGCACACCATAGAAG                         GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC
genomic: GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCC

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: 41 (upstream exon), 55 (downstream exon)
Score: 73

GGTCCATCTGCTCCATGGAGGCACACCATAGAAGgttggttgtc ... ctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC
                                           ttctgat  putative branch site (score: 73)
     ttaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaatattttaaaaaatttcatgactgtatgcattttcatatgtaaggattaaaaattggtcgtaggttccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC

- - - - - taaaaaa
- - - - - - - - -tttcatg
- - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - catatgt