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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttaggaccagtttatgtatatatattaataacttagctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc...

Basic information

species Oryza sativa
transcript LOC_Os02g21970.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 5'ss of exon 2
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttaggaccagtttatgtatata-tattaata--acttagctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc
 |||||||| || ||||| |||||||| || ||||| || || || ||||| ||||||||||| |||||||| |||||||| ||||||||| |||| |||||| ||| ||||  |        |||| |   ||||  | ||   |        | ||    |    |||| | | |  | | || ||   | ||     |  
TACTGGCAAGACCATGCTTGCCAAAGCAGTCGCACATCATACCACCGCTGCTTTTATCAGAGTCGTTGGTTCGGAGTTTGTACAGAAGTACTTGGGCGAGgtaagttgggacatgggagctattataatgccaatatgaattcttttggattggatataaaatgtagtgaattcataggtatggcgtt--gcctaggtcctg-

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 2
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttaggaccagtttatgtatatatattaataacttagctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc--------
 |||||||| || ||||| |||||||| || ||||| || || |||||||| |||||||| || || |||||||||||||| || |||||| ||||||||||| ||| ||| |  || | ||    |||| | |   || |     | | || |   |||    |||| | |   ||   |   ||   ||||  ||||         
TACTGGCAAGACCATGCTTGCCAAAGCAGTTGCACATCATACCACTGCTGCTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttgggagctattga-gtcccaatatgactccttttg--agttggatataaaatgt--agtgaactgatgcat---gttataagattaatgggttagtttatgc

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA11G31470.1 (Glycine max), 5'ss of exon 2
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatg----ttaggaccagtttatgtatat---atattaataactt---agctcactc-gttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc
 ||||||||||| ||||| ||||||||||| ||  | || || ||||| || || ||||| ||||| || || ||||||||||| ||||| || |||||||||||    ||| | |   || || |  ||   || || | ||  |   | || |||| | ||  | |  |||  |    | | || | | |  ||  | ||         
CACTGGCAAAACAATGCTTGCCAAAGCTGTTGCTAATCATACCACTGCCGCCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAGgtatgatttttaagtcatcttcatttggatgcgatgttgacaatgttgtaacttactctgctatctttgtttcttt---ttgaaaattatgggtttccaattc--------

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA11G31450.1 (Glycine max), 5'ss of exon 2
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatg---ttagg--accagtttatgtatat-atattaataactt---agctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc
 ||||| ||||| ||||| ||||||||||| ||  | || || ||||| || || ||||| ||||| || || ||||||||||||||||| || |||||||||||   ||| |  | | |  | || ||   || || | ||  |   |||| |||| |   |||||  |  ||    | | || | | |  ||  | || |       
CACTGGAAAAACAATGCTTGCCAAAGCTGTTGCGAATCATACCACTGCCGCCTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAGgtatgattttaagtcatctgcatttggatgcgatgttgacaatgttgtagcttactc-tgctatcttagtttctttt-tgaaaattatgggtttccaattca-------

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 2
-AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgtt------aggaccagtttatgtatat-atattaataactt---agctcactc-gttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc
  ||||||||||| ||||| ||||||||||| ||  | || || |||||||| || ||||| ||||| || || ||||||||||||||||| || ||||||||||  |      |  | | |  |||| || | || || | ||  |   |||| |||| | ||  | |  |||  |    | | || | | |  ||  | ||         
GCACTGGCAAAACAATGCTTGCCAAAGCTGTTGCGAATCATACCACTGCTGCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcatttttatatcatctgcatatggatgtgatgttgacaatgttgtagcttactctgctatctttgtttcttt---ttgaaaattatgggtttccaatt---------

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 2
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttaggaccagt-ttatgta--tatatattaataactta-gctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc
 ||||| ||||| ||||| || || ||||| ||| | || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||  ||||||||||||| |  ||  | | |||| |   |  | ||     |  |  | | |  | |       |     ||| |||  || | |     |||| | |  |   || 
CACTGGTAAAACCATGCTTGCTAAGGCTGTTGCAAATCATACTACTGCTGCTTTCATCAGAGTTGTGGGTTCAGAATTTGTTCAGAAGTATTTGGGTGAGgtatgcttagaataatattatcttgttgaaaataggccatgtgtgtttatgcttccttaactacatcctgtaatggcagacc---atttattcatttatcttt-

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|58678900|gb|CK067587.1|CK067587
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29656423|gb|CB652698.1|CB652698
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|58673134|gb|CK061820.1|CK061820
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29656424|gb|CB652699.1|CB652699
EST:     CAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29683628|gb|CB679903.1|CB679903
EST:     GTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: GTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|25798027|gb|CA753988.1|CA753988
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29659073|gb|CB655348.1|CB655348
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29636555|gb|CB641564.1|CB641564
EST:     AGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: AGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29624298|gb|CB629309.1|CB629309
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
EST: gi|29628785|gb|CB633796.1|CB633796
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGAT
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGAT
EST: gi|29624228|gb|CB629239.1|CB629239
EST:     CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAG                         GGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA
genomic: CATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCA

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: 75 (upstream exon), 67 (downstream exon)
Score: 79

AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttagg ... atttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGGCAAAACTATGCTCGCCAAAGCTGTGGCACACCACACTACTGCTGCATTTATCAGAGTTGTTGGTTCAGAGTTTGTGCAGAAGTACCTGGGTGAGgtatgttaggaccagtttatgtatatatattaataacttagctcactcgttacatcttgttcgctgaaataacaaatctagccttatacttaaaaggttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT