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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

Basic information

species Oryza sativa
transcript LOC_Os12g08830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
                || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||||||
----------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G425136_T01 (Zea mays), 3'ss of exon 1
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA-
                            | | || |    | |  |     | |   |   | || || ||||||||||||||   | | |     || |||||||||||||||| ||| | ||||||||||||||||||||||| || |||||||| |||||||| |||||   ||   |||     | | ||| |||  |||| 
---------------------------gtgagctcttcttcttctttctctacagtgaaatattgttgaattgttttcatgatgctgatcgaatcgtttagacagGTTGGAGAACGTACTGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATGTGCTGTGGCTGTGCGGCT-GTGCTGGTGGGGAG

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttg-----ttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
                || |  |     || |||||      |  | |||| |   ||  | ||| || ||||||||||||||   | | |     ||||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || ||||    
----------------gtgagctcttcttcttctttttcttct-ttctctgcagtgaaata-ctgttgaattgttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
----gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
      |   |   ||| |||   | | ||  |  |   |   |      |        || | || ||    | |||   || |      |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |||||
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggcaagt----atttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatata-gtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
 |||       ||  | |  || || | |||| ||    | |    |  | || |     ||     |     |  |   |  |    |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| |   | |  |||||
-taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

upper sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaa-aggaactgctggattgttttcatgatatagtt----tgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
    | |  || ||| | | | |    ||    | |  |   ||   | ||| |  | || |  ||     |||||    | || || ||    || ||||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || || || || |||  |||    |||| | | |  ||| |
----cataaatctttaggctt-tggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA

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|88579972|gb|CI691969.1|CI691969
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCG
EST: gi|66928198|gb|CX115046.1|CX115046
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|38478054|gb|CF962187.1|CF962187
EST:     TGTCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         A
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacag-
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         A
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacag-
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         A
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacag-
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         A
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacag-
EST: gi|33664741|gb|CF295708.1|CF295708
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|88381593|gb|CI682257.1|CI682257
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|33801711|gb|CF326727.1|CF326727
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|88432895|gb|CI690751.1|CI690751
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGG
EST: gi|88351000|gb|CI620660.1|CI620660
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCC
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCC
EST: gi|88433746|gb|CI582068.1|CI582068
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|14571429|gb|BI118797.1|BI118797
EST:     GGGCCTTCTGGCTGGGAGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGCTG
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTG
EST: gi|88429169|gb|CI690057.1|CI690057
EST:     GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAG                         GTTGGAGAACATACCGTAGGCCAGACGA
genomic: GGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGA

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), 74 (downstream exon)
Score: 44

TGTGGAGTTTCAGTGTTTGGTTTTGCAGGTGAGAGCATGGCAGTGAAGCAGGGCCTTCTGGCTGGGCGGATCCCTGGGCTCTCTGACCCTGATGAAAAAGgttggttctt ... gttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
                                          tttgttc  CT-rich tract
                                    atatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- -gcttcca
- - - - - - - - - - - - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg