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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g03020.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G176820_T01 (Zea mays), 5'ss of exon 2
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagc----ttaaaatcgtcaattccact--gaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag
||||||||| || ||||||||| | |||||||||||||||||||||||||||||||| ||| |||||||||||||||| ||||||||||||||||| ||||||||      |||    |||  | | |||  |       | ||  ||  ||  ||  | ||| |  || ||||  |  ||   ||||| | |  ||||||||
TGCCAAGGGAGTCAACATCATGGCGTTCTGCAAGGAGTACAATGCCAAGACGGCCGACAAGCCCGGCTACATCATCCCCGTCGAGATCACCGTGTTTGATgtgagtgagactaatgctgtccgtcctactttgggcagaagcgagaatcgattgctgttatggttg-tcataatgctg-gttactttgcttcgcattttgcag

upper sequence: LOC_Os03g03020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv02s0025g02890.t01 (Vitis vinifera), 5'ss of exon 2
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag
| ||||||||||||| |||||| | ||||| ||||| |||||||| | ||| ||||| ||||| |||||  | || ||||| || || || || | ||||||| | ||       ||   ||  | |  |    || ||  || ||    ||  || | |    |   |  | || |  | |  || ||  | ||||
TTCCAAGGGTGTGAATATCATGGCTTTCTGTAAGGATTACAATGCTAGGACCGCCGACAAGGCTGGCTATGTTATTCCTGTTGAAATTACGGTCTACGATgtgggtttctcgctttcttgtcttccg--tccccgtaaatttggat----aaattgagcagcttt---tgaaggtttcgtggtttgtttgctcgcag

upper sequence: LOC_Os03g03020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S141_43V6.1 (Physcomitrella patens), 5'ss of exon 2
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgag---cttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag--
| ||||||| || ||||| ||| | |||||||||||||||||||| ||||| || || ||| |||||||||| || || ||||| || || || |  ||||| ||   ||  |  |  |||      ||  ||  ||  |    ||  || |    ||   |  |   | |   |||    |||   || |  ||||     
TTCCAAGGGAGTTAACATTATGGCATTCTGCAAGGAGTACAATGCGAAGACTGCAGACAAGCCCGGCTACATTATTCCCGTCGAAATTACAGTTTATGATgtaagagactctaccttctcatcgtgtcttgataagttcgg--gtgattcccattagtccatggttggattcgaatgctattttatttgttcatttgtgttt

upper sequence: LOC_Os03g03020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S46_69V6.1 (Physcomitrella patens), 5'ss of exon 2
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagct-taaaatcgtcaattccactgaatgt-gtgtgaacatgcatctctaatgtgggtactcctaattatatgtg-tgtttgcctggttttttgcag
| |||||||||| ||||| ||| | ||||||||||| || ||||||||||| || || ||| | ||||| |||||||| ||||||||||| || | ||||||  |   |   | ||||  |||  |      | |||   |  |   |    | |   | ||  |  ||||  |  || || |     |  ||       
TTCCAAGGGTGTCAACATTATGGCTTTCTGCAAGGAATATAATGCCAAGACTGCTGACAAGCCTGGCTATATCATCCCCGTCGAGATCACAGTTTACGATgtatgtggttccagcgtcttttcttcgttccctagtgctcatttttgtagtgatttatgttagactgaattgaaaatgctgctcatacgcattgcaatga

upper sequence: LOC_Os03g03020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ32645 (Selaginella moellendorffii), 5'ss of exon 1
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag
| ||||||| || ||||||||| ||||||||||||| ||||| |||| ||||||||| |||||||||||||| ||||| || ||||| || || ||||| |||||||  |  ||     | | | |  | |||  |||| |||   | | ||||  |                                        
TTCCAAGGGCGTTAACATCATGGCCTTCTGCAAGGAATACAACGCCAGGACGGCCGACAAGGCCGGCTACATTATCCCCGTGGAGATTACAGTCTTCGACgtgagct--acctctctcctcctagtcga-gtgactgaa-atgtcgc-caaatgcag----------------------------------------

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|38473172|gb|CF957304.1|CF957304
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|38471941|gb|CF956072.1|CF956072
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATNAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|38476622|gb|CF960755.1|CF960755
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|7378433|gb|AU088704.1|AU088704
EST:     AGAAGCCCGGCTACATCANCCCTGGTCGGAGATCACCGTTTTCGAT                         GATAAAAG-TTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: AGAAGGCCGGCTACATCATCCCT-GTC-GAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|38470412|gb|CF954543.1|CF954543
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|58690577|gb|CK079264.1|CK079264
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|15008426|gb|AU222814.1|AU222814
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTC
EST: gi|88341000|gb|CI638556.1|CI638556
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCT
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCT
EST: gi|88962778|gb|CI023878.1|CI023878
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|88324214|gb|CI563825.1|CI563825
EST:     CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
genomic: CGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTC
EST: gi|86902910|gb|CI312287.1|CI312287
EST:     CATCATCCCCTGTCGAGATCACCGTGTTCGAT                         GATAAAAGTTTCACCTTTATNCTTGAAGACCCCTCCCTGCCTCAGTCCTTC
genomic: CATCAT-CCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTAT-CTTGAAGACCCCT-CCTGCCTCAGTCCTTC

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: 57 (upstream exon), 74 (downstream exon)
Score: 33

TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaa ... ttttttgcagGATAAAAGTTTCACCTTTATCTTGAAGACCCCTCCTGCCTCAGTCCTTCTCCTCAAGGCAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAAGGGTGTGAACATCATGTCCTTCTGCAAGGAGTACAATGCCAAGACGGCCGAGAAGGCCGGCTACATCATCCCTGTCGAGATCACCGTGTTCGATgtgagcttaaaatcgtcaattccactgaatgtgtgtgaacatgcatctctaatgtgggtactcctaattatatgtgtgtttgcctggttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA