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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtaacctgcatataatgattctccattcaataagtttatgtctcacatctactttttgcggggtcatgtctcacatctacttcaccttgctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG

Basic information

species Oryza sativa
transcript LOC_Os06g01850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 3
------------------------------------atgtaacctgc-atataatgattctccattcaataagttta--tgtctcacatct-actttttgcggggtcatgtctcacatctacttcaccttgc--taatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG
                                      | | |   |   ||  |  |||| ||     | |  | |  ||  |  || |  | | | ||      | |||  | | | | | |   | | |  ||||  ||||||  |  |||| |||  | | ||| ||||||| |||||||| |||||||||||||| ||||||||||| || || ||||  |||||||||
gtacgtctacgtctcttcacatcccgcgctgcaccagagcaccacactgcattcttcttctacaaatcctgatctgacttgattggcacccgaatgtctgatccagcttgttccccctgtgcgtgctcataccataatgcagGTGATCTTCAGCCAGGTGATAACGTCCAGATAACAGGACCAGTCGGCAAAGAAATGCTGATGCCCAAAGACCCAAACGCTACCATTATAATG

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 4
atgtaacctgcatataatgattctccattcaataagtttatgtctca-catctactttttgcggggtcatgtctcacatctacttcaccttgctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG
              |||  |      |  ||||  || | ||    | | | |||  |||         |   |    | |          | |  |  ||||||||||||||| |||  ||| |  ||||| || ||||| || ||||| |||||||| ||||| ||||| |||||||| |  || || |||
-------------gtaagaaagaagaa--caatgtgtctgtgatggatcgtttacggttta---aactgttcttagtgtttgtgatgttcgggtttttcagGTGACTTGAAGCCGGGTGATGAAGCTAAGATCACTGGACCTGTTGGCAAGGAAATGCTTATGCCAAAAGACCCCAATGCCACCATCATCATG

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 3'ss of exon 4
-----atgtaacctgca-tataatgattctccattcaataagtttatgtctcacatctactttttgcggggtcatgtctcacatctacttcaccttgctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG
     ||  || | ||  ||| |  ||      | | ||  |     || |   |  | ||||       |||    ||  || ||   | | | |  |  |  ||||||||||||||||||  |||||||||| || || ||||| || || ||||||||||| ||||| |||||||| ||||| | | | ||||||
tttgtatagaatcagctctatcagcatcggtgctacgatggggccgagtttaggaaatgctttgattatcgtc----ctagcaact--ctgatccttttgtttcagGTGACTTGAAGCCTGGGGCTGATGTCAAAATCACAGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACTGTCATAATG

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|29659028|gb|CB655303.1|CB655303
EST:     GACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: GACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88671965|gb|CI726081.1|CI726081
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|58695210|gb|CK083897.1|CK083897
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88671055|gb|CI725171.1|CI725171
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCCAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|29683077|gb|CB679352.1|CB679352
EST:     CGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88668144|gb|CI722883.1|CI722883
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGCTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88955314|gb|CI721886.1|CI721886
EST:     ACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTA
genomic: ACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCC-TCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTA
EST: gi|29683657|gb|CB679932.1|CB679932
EST:     CGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88955313|gb|CI721885.1|CI721885
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCA
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCA
EST: gi|33798466|gb|CF325091.1|CF325091
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|29685686|gb|CB681961.1|CB681961
EST:     AGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: AGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|29685685|gb|CB681960.1|CB681960
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88665792|gb|CI715948.1|CI715948
EST:     CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCCAGATAACCGGACCACTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
EST: gi|88670049|gb|CI724165.1|CI724165
EST:     CACCAACGACCAGNGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT                         GTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG
genomic: CACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAG

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: 125

GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCTgtgagttcgt ... gctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatctactttttgcggggtcatgtctcacatctacttcaccttgctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG
                                            tgctaat  putative branch site (score: 125)
                                         ccttgct  CT-rich tract
                                               taatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtaacctgcatataatgattctccattcaataagtttatgtctcacatctactttttgcggggtcatgtctcacatctacttcaccttgctaatatagGTGACTTGAAGCCTGGTTCTGATGTCAAGATAACCGGACCAGTAGGCAAAGAAATGCTCATGCCCAAAGATCCCAATGCTAATATTATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -acctgca
- - - - - - - - -tgattct
- - - - - - - - - - - - ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcacc