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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctaacccacaactctgaagttattgtagtgcattattatttttttctgttctagaagattgatcctgactaatggttgagagttacgatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG

Basic information

species Oryza sativa
transcript LOC_Os01g38620.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------gtgcctaacccacaactctgaagttattgtagtgcattattatttttttctg-ttctagaagattg--atcctgactaat--ggttgagagttacga---tattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
                                                                 ||||||||      | |    |  | ||    |||  | ||   ||||| |  || ||| ||||||  | | |||||||   | || |   |||  |   | ||||||||| ||||||| ||||||||||||||| |||||||||||||||||||||||
gtaagcccgcacttgagtctgatcatatcaccaaagttattcatgattgtaaaagggacagtgaggtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142984_T02 (Zea mays), 3'ss of exon 3
gtgcctaacccacaactctgaagttattgtagtgcattattatttttttctg-ttctagaagattg--atcctgactaat--ggttgagagttacga---tattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
||||||||      | |    |  | ||    |||  | ||   ||||| |  || ||| ||||||  | | |||||||   | || |   |||  |   | ||||||||| ||||||| ||||||||||||||| |||||||||||||||||||||||
gtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 3
gtgcctaacccacaactctgaagttattgtagtgcattattatttttttctgttctagaagattg--atcctgactaa-tggttgagagtt-acga--tattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
||||||||      | |  ||| || | |      ||  ||  |||||    || ||| ||||||    | ||||||| | ||| ||| || |  |  | ||||||||| ||||||| ||||||||||| ||| |||| ||||||||||||||||||
gtgcctaattatgcattgggaacttttagcttgctatgttttctttttgtccttttaggagattgtagacttgactaactagtttagactttatcactttttgcagGCTTTGTATTTTCAGTTTGGCATCAAACTGCACAATGTGATGGATACACAG

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g02690.t01 (Vitis vinifera), 3'ss of exon 5
gtgcctaacccacaactctga-agttattgtagtgcattattatttttttctgttctagaagattgatcctgactaatggttgagagttacgatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
        | |||||    |   |||| | || ||  || |   |    | |  ||   |   ||  | || |    | | | |   |  | ||  ||||||| |||||||| ||||||||||| || |||||||||||  ||||| | |||
------gtctcacaaaatagttggttacttta-tgtgttctagataacatgttctc---acattttctgcttatctttagct-attttccctattgtgcagGCACTGTATTTTCAGTTTGGCATCAAGTTGCATAATGTTGTGGATTCTCAG

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|218487804|gb|FG952787.1|FG952787
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|58594793|gb|CF993101.1|CF993101
EST:     AGGCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|27577389|gb|CB000084.1|CB000084
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218504651|gb|FG960768.1|FG960768
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218486574|gb|FG956238.1|FG956238
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTC
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTC
EST: gi|33795398|gb|CF323569.1|CF323569
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|38472674|gb|CF956806.1|CF956806
EST:     CAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: CAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|86908033|gb|CI298799.1|CI298799
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|27577966|gb|CB000661.1|CB000661
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218495275|gb|FG966279.1|FG966279
EST:     GTCAGAATATGTCACCAAAGTTATCTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: ATCAGAATATGTCACCAAAGTTAT-TCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218500721|gb|FG955417.1|FG955417
EST:     TCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: TCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|33793613|gb|CF322690.1|CF322690
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|38473357|gb|CF957489.1|CF957489
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|38478638|gb|CF962771.1|CF962771
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         T
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcag-
EST: gi|38478638|gb|CF962771.1|CF962771
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         T
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcag-
EST: gi|58588638|gb|CF986946.1|CF986946
EST:     AGGCAGAATATGTCACCAAAGTTATTCATGACTGCCAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|313080792|gb|HO213589.1|HO213589
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|27577933|gb|CB000628.1|CB000628
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACCCTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|58598824|gb|CK009352.1|CK009352
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218483500|gb|FG948234.1|FG948234
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|25801465|gb|CA757426.1|CA757426
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|218502513|gb|FG958404.1|FG958404
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgttctagaagattgatcctgactaatggttgagagttacgatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
                         gactaat  putative branch site (score: 2)
                                              atatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctaacccacaactctgaagttattgtagtgcattattatttttttctgttctagaagattgatcctgactaatggttgagagttacgatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA