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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
-gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccact-cgatctggaatggaagctaggttcaatctggggagtata-atatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
  |  ||   || | |    | |    |  ||   |||   ||   |  | |  |||   || |  |   ||  | ||    ||     | |||| |     || ||  |    || |||     | |       |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 1
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
||     |  |   ||  |    ||||  | |  || |  |     |    ||| || |    |  |||   |        |    | |||| |     || ||  |    || |||     | |       |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
gtagtttcctctgggagtttcggttaaattcgg-ttgtggtgaggacatgatgggatcgtctgtttgtttggt--------tcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
gtgagcgcgccctcgaactcgccttaaccttgtctt--atcctccactcgatctgg----aatggaagctaggttcaatc--tggggagtataatatctgggggt-tggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
|| |     |  | |  ||  || ||   |  |||   |   ||   |  ||  ||      ||    |  | |   |||    |   || |  |  ||| |  | ||   || | ||  ||    |    ||        |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
gtaactatccatttg--cttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccact-cgatctggaatggaagctaggttcaatctggggagtata-atatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
    ||   || | |    | |    |  ||   |||   ||   |  | |  |||   || |  |   ||  | ||    ||     | |||| |     || ||  |    || |||     | |       |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
--ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

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|88342082|gb|CI644419.1|CI644419
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGNGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|44677691|gb|CR291125.1|CR291125
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88424666|gb|CI606465.1|CI606465
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88389277|gb|CI598075.1|CI598075
EST:     CTAGGAGCGGCGGGGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGGGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88718825|gb|CI742335.1|CI742335
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|117245193|gb|CT843395.1|CT843395
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88391585|gb|CI600774.1|CI600774
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88396101|gb|CI595649.1|CI595649
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88370889|gb|CI595001.1|CI595001
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88718610|gb|CI742120.1|CI742120
EST:     CTAGGAGCGGNGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88368924|gb|CI635234.1|CI635234
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|86902238|gb|CI302269.1|CI302269
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88729100|gb|CI752610.1|CI752610
EST:     TAGGAGCGGCGGCGGGTGCCGTCGTCTTGCTGCTTCCCCTTCCGCCTCCG                         GTCCACCC-TGCAGGCGGCGATGGCGTCCTTCCGGGGCCTGACCGCGGTTT
genomic: TAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCC-TTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88439183|gb|CI604468.1|CI604468
EST:     CTAGGAGCGGGGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGAAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88422482|gb|CI571464.1|CI571464
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|33793807|gb|CF322790.1|CF322790
EST:     TGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: TGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|86900894|gb|CI304099.1|CI304099
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|86901424|gb|CI308405.1|CI308405
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88727820|gb|CI749332.1|CI749332
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88352129|gb|CI613780.1|CI613780
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88352215|gb|CI613866.1|CI613866
EST:     CTAGGAGCGGGGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
EST: gi|88315947|gb|CI618823.1|CI618823
EST:     CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG                         GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTT

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: 36 (upstream exon), 48 (downstream exon)
Score: 2

GTCCGTCTTCCCTCCCGGCCTCGGATCCCGGAGGAGGTCTCTCCTCCTCGCTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... caactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
                 agtataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttagGTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT