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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatttaacctgagaacggtccttataaatgtcactcatcagttgtcatttgtgcatttgagtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT

Basic information

species Oryza sativa
transcript LOC_Os03g55850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G040030_T01 (Zea mays), 3'ss of exon 1
-----tacatttaacctgagaacggtccttataaatgtcactcatcagttgtcatttgtgcatttgagtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT
     || |    |  |      |   ||  ||        |  | || | |  ||    |     | || | || |||  |  ||||||||| ||| ||| |||||| ||| ||||||||||| | ||||| |||||||||||||||||||| ||||||||||| |||||||||||||| || ||||||  || |||||| |||
gaatttataagctattttcacctgacactggtaggaccattttgtaaggtat--ttctcactaccaattaatcga-tga--caactctgttctattccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT

upper sequence: LOC_Os03g55850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052423_T01 (Zea mays), 3'ss of exon 1
tacatttaacctgagaacggtccttataaatgtcactcatcagttgtcatt-tgtgcatttgagtatttgactga-accccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT
||    |    ||   |||   | | |   || |||  | || || | |   | |   |      | || | ||    |  ||||||||| ||| ||| |||||| ||| ||||||||||  | || ||||||||||||||||||||||| ||||||||||| |||||||||||||| || ||||||  || |||||| |||
tattacttggttgtatacgagacgtcttg-tggcacg-accatttcttaaggtatttctcgctacaattaattggtgacaactctgttctgttccactacagGTATCTCTTGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCT

upper sequence: LOC_Os03g55850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0207g00220.t01 (Vitis vinifera), 3'ss of exon 1
---taca-tttaacctgagaacggtccttataaatgtcactcatcagttgtcatttgtgcatttga-gtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT
   ||   ||| | |   |  |  |||| |   || | | |  |||   | ||  | ||||  ||| || | | |   |||      | | |   | |||||||| ||  |  ||||| ||||| ||||||||||||  ||||||||||||||  | || ||||| ||||||||||||||||  || |||  ||   |||||   
agctatggtttgatccctgtgca-tcctgaagcatatta-tgttca--cgccaact-tgcaggtgaagtttataaactaacaaatattttacatgtttactgcagTTATTTGTTGATACTGGATCGGACAAACTGGAGAACCAACATGCTGACTTCGCTTTTGGTTCCTTACATTTTCTTTAGTCTTCCTCCTGTATTGTTCAAC

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|29656136|gb|CB652411.1|CB652411
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|569927|gb|D40776.1|D40776
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|88669180|gb|CI720137.1|CI720137
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGANAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|88825479|gb|CI776044.1|CI776044
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|29667854|gb|CB664129.1|CB664129
EST:     AGTGGCTCGCCTTTTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: AGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|58591798|gb|CF990106.1|CF990106
EST:     CTCGGATTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCGGGCATGCTGACCG
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACC-AACATGCTGACCG
EST: gi|29667853|gb|CB664128.1|CB664128
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|58591068|gb|CF989376.1|CF989376
EST:     CTCGGATTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGAGCGACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|568835|gb|D39684.1|D39684
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|58586796|gb|CF985104.1|CF985104
EST:     CTCGGATTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAAGGGTGCTGACCG
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAA-CATGCTGACCG
EST: gi|66913495|gb|CX100343.1|CX100343
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|88736312|gb|CI759820.1|CI759820
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGANAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|218480554|gb|FG955808.1|FG955808
EST:     CTCGGATTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|88733267|gb|CI756444.1|CI756444
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
EST: gi|88407922|gb|CI588951.1|CI588951
EST:     CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGT                         GTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC
genomic: CTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGC

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: 62 (upstream exon), 75 (downstream exon)
Score: 38

GCGTGGCGGCGCGGAAGCTCGCCAACCACGCGCTCGTCCTCGGCGGCGGCCTCGGGTTCGGCACCACCTTCCTCAAGTGGCTCGCCTTCTTCGCCGCCGTgtgagtcacc ... tctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatttgtgcatttgagtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT
                   atttgac  putative branch site (score: 38)
                              ccccctctgttctctt  putative PPT
                agtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatttaacctgagaacggtccttataaatgtcactcatcagttgtcatttgtgcatttgagtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg