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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacattaaaacaccatagtattgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA

Basic information

species Oryza sativa
transcript LOC_Os06g34690.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 13
gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacattaaaacaccatagtattgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
    |  ||| | |  ||||||||    ||||   |    |  |  |||| | ||  |  ||   ||| | | ||| |   |   ||||||||||||| |||||||| || |||||||||||||||||||| || ||||| |||||||||||| | || ||||| ||||| ||||||||||||||||
----gtatttctttttatgtgcacaaaagcatgcctgac-caatgtttgtttgcatgtctaa---ccacaatgttgtcc-attttagATCTGGGATTCCTACAGTGTTAAAGCACAAACGTTCAAGACAGCAATTGAGGCTGCTTGCATGCTTTTGAGAATCGATGACATTGTCAGCGGTATCAAGA

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 13
gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacattaaaacaccatagtattgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
        ||  || ||| |||||   ||||  | |    | ||  |||| | ||  |  |||  ||| | |     |   |   ||||||||||||| ||||| || || || || |||||||||||||| || ||||| |||||||||||| | || || || ||||| ||||||||||||||||
-----gtattcccttcatctgcacaaatgcaagt-ttgaccattgtttgtttgcatgtctaaatgccacaatg----cccattttagATCTGGGATTCCTACAGCGTTAAAGCGCAGACGTTCAAGACAGCGATTGAGGCTGCTTGCATGCTTTTGAGAATAGATGACATTGTCAGCGGTATCAAGA

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 10
--gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacatta------aaacaccatagtattgcctt-----gtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
   |    |    | | |||   |  |  ||  | |||  |   |||| |  | | | || |       || || |   | ||   |       |   ||||||||||| |||||| ||| || |||||||| || ||||| || || || || ||||||||||||||  |||| || ||  | || || || |||||||
acctaatacaagatttacattctctgtcttgtttctatgattactttgataagcatagatgattggatgaatactaagatgtttgttataatgattttagATCTGGGATGCTTACAATGTGAAAGCACAAACATTTAAGACTGCCATTGAAGCTGCTTGCATGCTTCTGCGGATTGATGATGTAGTGAGTGGGATCAAGA

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------gttggcctttttctccatgtgcactgctgcatatatcct-gcttttgttgtgtacacattaaaacac-catagtat-tgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
                        |     |   | || |  |||    |    |  ||  | | ||||||| |  |    | |||      |  | ||     || |  ||||| |||||| |||| | ||| |||||||| || || ||||| || |||||||| ||||||||||| |||||||||||||||||||| || || || || |
gttcgagattttcttctcctataatcctattcactttctaattgcttcacaatttggatttttgtttttgtttttaatttgtgaaactggatactgcatacatatttttccagATATGGGATGCTTATAATGTGAAGGCACAGACCTTTAAGACCGCCATCGAGGCTGCTTGCATGCTGCTTAGGATCGACGACATCGTGAGTGGAATAAAAA

upper sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
gttggcctttttctccatgtgcactgctgcat--atatcctgcttttg-ttgtgta-cacattaaaacacca-tagtattgccttgtc----------gcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
  ||  ||  ||||     | | ||      |   |    || || || |||  || || | |   |      ||||| | |||   |           ||||| |||||| |||||| ||| |||||||| || || |||||||| || || || ||||||||||| ||||||||||| ||||| || ||||| |||||||
--tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA

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|88903041|gb|CI088579.1|CI088579
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|89179006|gb|CI043511.1|CI043511
EST:     AAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: AAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|8527364|gb|AU092179.1|AU092179
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTNTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|89185732|gb|CI047601.1|CI047601
EST:     TGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|86481791|gb|CI124424.1|CI124424
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|8527533|gb|AU092348.1|AU092348
EST:     TTGGCATTGACGGAAGGANCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|218482787|gb|FG945649.1|FG945649
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|27576407|gb|CA999101.1|CA999101
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|29661338|gb|CB657613.1|CB657613
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG
EST: gi|218479881|gb|FG966071.1|FG966071
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCT
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCT
EST: gi|25806437|gb|CA762398.1|CA762398
EST:     TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG                         ATCTGGGATTCTTACAGTGTCAAGGCGCAAACGTTCAAGACAGCTATCGAG
genomic: TTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAG

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: 72 (upstream exon), 71 (downstream exon)
Score: 55

CATGCAAATGGTGAAAATGCGTGGGTTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAGgttggccttt ... cttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcctgcttttgttgtgtacacattaaaacaccatagtattgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA
                                         ttgcctt  CT-rich tract
                      acattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcctttttctccatgtgcactgctgcatatatcctgcttttgttgtgtacacattaaaacaccatagtattgccttgtcgcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT