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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA

Basic information

species Oryza sativa
transcript LOC_Os12g14070.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 1
-acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
     ||    |||    | |||  | |   | || ||  |  ||||||| || |||||||| | |   | | || ||  | | |    | |    ||||||| ||||||||||||||||| ||||||||||||||| | ||||| ||||| || |||||||||||||| || || |||||||||||||| ||||| ||||
agttgctactagctaccagaccaata-gatgtgatatacttaccattttacttccatagtaagttgtacatttaacttatcctgttttattatccgaacagGTTTTGAGGAAGTTGGTGGATGATGCATCTAAGTTTCTTAATGAGAAAATCACAAAAGCAGTGGTTACAGTCCCAGCATACTTCAATGATTCACAAAGGA

upper sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 1
acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatgg-attactaaattt-cacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
    |||  |  |   | |  |   |         ||  || |  | || |   ||  | | ||  |  |  |  |||  ||| ||    |  ||   | ||||  | |||||| | ||||| ||||| || ||||||||||| || ||  ||||||| || || |||||||| ||||| |||||||||||||| || ||||
--gtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA

upper sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 1
acacctgaatgctcagggtccataatggc---ataatgtagcttacattttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
 | | |   | |||    |   || ||     | | | | |||||   | || |    |  |   ||| |||   |||      | || | |   |  |  ||||  | || ||| | || || ||||| || |||||| ||||||| ||| | || ||||| ||||| || || ||||| |||||||||||||| |||||||
-ctcttcgttcctccacttttttagtgattgaaaagtttggcttattatataatgtttttatttttgggttagctaataattggtctctgtttctt--attagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTCACAAAAGCTGTGGTCACAGTGCCTGCTTACTTCAATGACTCCCAGAGGA

upper sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ09963 (Selaginella moellendorffii), 3'ss of exon 2
acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaa-atggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
                         ||   |||| ||   | |  |||  |    |  |||  | || |  ||  |||    ||||       |    ||||| ||||| ||| |||| ||||| || || ||||||||||| |||||| | | ||| || ||  | ||||||||||| ||||||||||| || ||||| |
------------------------gtga-gtaatctattcttctctttggtctgctgttaacgttgagtgatacgttttttctttc--tcttgtttggcagGTTTTGAGAAAGCTGGTCGACGACGCTTCCAAGTTTTTGAACGACAAAGTGAACAAGGCTGTCATCACTGTTCCTGCTTACTTCAATGATTCCCAGAGAA

upper sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ23703 (Selaginella moellendorffii), 3'ss of exon 1
acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
                           | | | |||  |||   |||  | | |   || || |   |   | |  |   || |        |    ||||| ||||| ||| |||| ||||| || || ||||||||||| |||||| | | ||| || ||  | ||||||||||| ||||||||||| || ||||| |
-----------------------gtgagtaaactgtt-cttctctttggtctgc--tgttaacgttgtgtgatacgtttgttctttctcttgtttggcagGTTTTGAGAAAGCTGGTCGACGACGCTTCCAAGTTTTTGAACGACAAAGTGAACAAGGCTGTCATCACTGTTCCTGCTTACTTCAATGATTCCCAGAGAA

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|58688010|gb|CK076697.1|CK076697
EST:     GCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: GCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|33799830|gb|CF325781.1|CF325781
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|29614003|gb|CB619016.1|CB619016
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|13420936|gb|AU175026.1|AU175026
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|29636280|gb|CB641289.1|CB641289
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|29613315|gb|CB618328.1|CB618328
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT
EST: gi|29631733|gb|CB636742.1|CB636742
EST:     ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAG                         GTCTTGAGGAAGTTGGTGGACGATGCATCTAATTTTTTGAATGACAAAATT
genomic: ACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATT

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: 73 (upstream exon), 75 (downstream exon)
Score: 193

GCAGGTCTCCTACCACGTCGTCCGCGACGACAACGGCAACGTCAAGCTCGACTGCCCCGCCATCGGCAAGCAGTTCGCCGCCGAGGAGATTTCCGCGCAGgtgatttctt ... aatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
                      tactaaa  putative branch site (score: 193)
                    attactaaatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatggattactaaatttcacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - -tgaatgc
- - - - - - - - - - - - -tggcata
- - - - - - - - - - - - - - - - - - -gcttaca