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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g14270.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 6
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
||||||| || | || | | |||| | | |||| ||| | ||| || | || || |||| |||| || |||||||||||||||| ||||||||||||||||| |||||||| || |||||||| ||||| || ||||||||||||||||| ||||||
gtacttatgtggttatttgttatgtagtttctatcatat--gattaataacat----gggtatataaattctaaaatgt--ccattgcagCCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 6
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
||||||| || | || | ||| | ||| || |||| || | ||||| | || |||| ||||| || ||||||||||||||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||||| ||||||||||| ||||||
gtacttatgtggttatttgttatgcggtctgtgtcgtag--gatggataacagcatgggttt-ataaattctaaaatgtg--cattgcagCCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgat-gtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
||| || | | | ||| | || ||| ||| || | | | || || || ||| || || || | ||||||||||| || ||||||||||||||||||||||||||||| | || |||||| | |||||||| |||||||| ||||||||| ||||
gtatttc-tcaattttttgtttccttgtgctgcatatgtatcatca-ctttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 6
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaa-atttctttgat-----gtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
| || | ||||| || || || | || | | ||| | || | | || | || || ||| | | ||||||||||| || ||||||||||||||||||||||||||||| | || |||||| | ||||||||||||||||| ||||||||| | ||
--------gtatttctcaattttttgtttcc--ttgtgctgcataaacatcactttatgctgtagttacttattagattaattgctgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatt------tctttgatgtgatttctgt-agCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
| |||| | ||| || |||| | || | | | || | || ||| | || | || | ||| ||||| | |||||||||||||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||| ||| |||||||| |||
---------gttcatacttgtctataattgatgtaaaatctaa--aatctcttgctgtgttccgtatttgctgatttttcgttgtcctttctcttagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacttaattgttataccattttatggtttatgttatatatgatg-agcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
|| | |||| || | || | | | || |||| | |||| || ||||||| | |||||| | | | ||||||||||||||||||||||| |||||||||||||||||||| || |||||||| ||||| |||||||| || |||||||| |||
gt-ttgaatttttttcttgcattgatgca-aaaccaaatctgatttatcgtc--tcgaggttttga-----ttttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 6
----gtacttaattgttataccattttatggtttatgttatatatgatgagc-gtcattctaggttttaaaatttctt------tgatgtgatttctg----tagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
||| ||| ||||| |||||| || | | ||| | || | | ||| | | ||| || || | || | ||| || |||||||| || ||||||||||||||||||||||| ||||| | ||||| || |||||||||||||||||||||||||||||| |||
gtaagtaattagaatttatagttcagtatggtaaat-tcttttataaggaaccataatttcatggggagaaacttgttactgaataatcagctttatgaccctagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACACCTCCAACAATAGCTAACCCTGAGTACAAGGGACCATGGAAGCCCAAG

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 6
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgatgtgattt----ctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
|| ||| ||| || || || | | | | || | || | | ||| | || | | | |||| | |||||||| || ||||||||||||||||||||||| ||||| || ||||||||| | ||||| |||||||||||||||||||||| ||||
-----gtatatttaatccaaattgtgattca----aaaggttttggttttagttttctgatttggtaattgactaaaattatttggaattatagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG

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|88729754|gb|CI753264.1|CI753264
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|163920423|gb|EG710621.1|EG710621
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|33793505|gb|CF322636.1|CF322636
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGAATGGTGAGTGGACTGCACCAACCAT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGA-TGGTGAGTGGACTGCACCAACCAT
EST: gi|88718533|gb|CI742043.1|CI742043
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|88722171|gb|CI745681.1|CI745681
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|29675378|gb|CB671653.1|CB671653
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|88691187|gb|CI735266.1|CI735266
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|58656433|gb|CK045113.1|CK045113
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|14192066|gb|AU184277.1|AU184277
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|33793940|gb|CF322858.1|CF322858
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGAATGGTGAGTGGACTGCACCAACCAT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGA-TGGTGAGTGGACTGCACCAACCAT
EST: gi|58596614|gb|CK007142.1|CK007142
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGGACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|88690114|gb|CI734193.1|CI734193
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|88730078|gb|CI753693.1|CI753693
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|66915891|gb|CX102739.1|CX102739
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|8856749|gb|AU094067.1|AU094067
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
EST: gi|58679227|gb|CK067914.1|CK067914
EST:     GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAG                         CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT
genomic: GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATT

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: 48 (upstream exon), 73 (downstream exon)
Score: 222

GGATACGATGATATTCCCAAGGAAATCCCTGACCCTGATGCTAAGAAGgtacttaatt ... atttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatgatgagcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG
                                   ctttgat  putative branch site (score: 222)
 tttctgt  putative PPT
 ttttaaaatttctttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA