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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactcaaatcttcattttcggaacctcttgtttagaaagaagtttttgctttctgtatggtgtctcaacctggacacttacatataatatgtgtttaattgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC

Basic information

species Oryza sativa
transcript LOC_Os01g59930.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 8
gtaaaactcaaatcttcattttcggaacctcttgtttagaaagaagtttttgctttctgtatggtgtctcaacctggacacttacatataatatgtgtttaattgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC
|| || ||  | ||||  ||||       |   ||| |  | |||| |      || |||||    |||| |       |  || |  | | |||||||||  | || |||||| |||| |||||||||||||||||||||||||| |||||||| |||||||| ||||||   ||||| ||||||||||||||||||||||||||  |  
gtgaatcttgagtcttatttttt-----tttcagttcactatgaagatc---gattgtgtat----tctctattcttgtatcta-acctgagatgtgtttacctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ07598 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaactcaaatcttcattttcggaacctcttgtttagaaagaagtttttgctttctgtatggtgtctcaac-ctggacacttacatataatatgtgtttaattgttc--cagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC
                                                |  |      |    |  |   ||| || ||  |    |   | | | | ||   |       ||||| ||||||||||| ||||||||||||||||| || |||||  | ||| | |||| |||||| ||| | ||||||||||| ||||| |||| |       
-----------------------------------------------gtacgtagcacgagaagaattcaaacgctagaagcgatgacgaactctattttctttcaacaaacagATTTTGAGGTGTGGACCTCCTCCGATGAACAAAGCGATGGCCACACACTTGGATGCGCTCGGCTACTCTAAGGAGATGCAATTCCAATTCTGAAAAGGGA

upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ10977 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaactcaaatcttcattttcggaacctcttgtttagaaagaagtttttgctttctgtatggtgtctcaacctggacacttacatataatatgtgtttaattgttc--cagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC
                                             ||   |       | |   | ||  || || ||  |    |   | | | | ||   |       ||||| ||||||||||| ||||||||||||||||| || |||||  | ||| | |||| |||||| ||| | ||||||||||| ||||| || |||       
---------------------------------------------gtacgtagcacgagaagaat-tcaaaagctagaagcgatgacgaactctattttctttcaacaaacagATTTTGAGGTGTGGACCTCCTCCGATGAACAAAGCGATGGCCACACACTTGGATGCGCTCGGCTACTCTAAGGAGATGCAATTCCAATTTTAAAAAGCGA

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|117244284|gb|CT843075.1|CT843075
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGAC-TTCAA                         ATCTTGAGGTGTGGTCCTCCTC-GATGAACA-GGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88200209|gb|CI200059.1|CI200059
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|15852322|gb|BI805118.1|BI805118
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|27576200|gb|CA998894.1|CA998894
EST:     CCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88201419|gb|CI201774.1|CI201774
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|3767653|gb|AU031680.1|AU031680
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAAT-GNTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88987863|gb|CI017952.1|CI017952
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88214448|gb|CI214297.1|CI214297
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|58689499|gb|CK078186.1|CK078186
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88832171|gb|CI017405.1|CI017405
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|11171266|gb|AU163705.1|AU163705
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88839184|gb|CI378108.1|CI378108
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88214584|gb|CI214433.1|CI214433
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|86883521|gb|CI338070.1|CI338070
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTC
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|58678583|gb|CK067270.1|CK067270
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|56158135|gb|C73512.2|C73512
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88992675|gb|CI035691.1|CI035691
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88848493|gb|CI087015.1|CI087015
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88847923|gb|CI006109.1|CI006109
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|86418467|gb|CI032676.1|CI032676
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|58608501|gb|CK036534.1|CK036534
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|88988656|gb|CI039075.1|CI039075
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT
EST: gi|86545731|gb|CI185937.1|CI185937
EST:     CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAA                         ATCTTGAGGTGTGGTCCTCCTCCGATGTACAAGGCAATGGCTGCGCACCTT
genomic: CACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTT

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: 70 (upstream exon), 52 (downstream exon)
Score: 18

CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAgtaaaactca ... attgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtatggtgtctcaacctggacacttacatataatatgtgtttaattgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC
                                              ttgttcc  CT-rich tract
                         ttacatataatatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactcaaatcttcattttcggaacctcttgtttagaaagaagtttttgctttctgtatggtgtctcaacctggacacttacatataatatgtgtttaattgttccagATCTTGAGGTGTGGTCCTCCTCCGATGAACAAGGCAATGGCTGCGCACCTTGATGAGCTCGGGTACACCAAGGAGATGCAGTTCCAGTTCTAAGCTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG