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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacccacaactctgaagttattgtagtgcattattatttttttctgttctagaagattgatcctgactaatggttgagagttacgatattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g38620.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G081924_T01 (Zea mays), 5'ss of exon 3
TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacccacaactctgaagttattgtagtgcattattatttttttctgttctagaagattg--atcctgactaa-tggttgagagtt-acga--tattgcag
||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||||||||||||||| || ||||||||||| |||||||||||      | |  ||| || | |      ||  ||  |||||    || ||| ||||||    | ||||||| | ||| ||| || |  |  | ||||||
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGCGAGgtgcctaattatgcattgggaacttttagcttgctatgttttctttttgtccttttaggagattgtagacttgactaactagtttagactttatcactttttgcag

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G142984_T02 (Zea mays), 5'ss of exon 3
TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacccacaactctgaagttattgtagtgcattattatttttttctg-ttctagaagattg--atcctgactaat--ggttgagagttacga---tattgcag
||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||||||||||||||| || |||||||||||||||||||||||      | |    |  | ||    |||  | ||   ||||| |  || ||| ||||||  | | |||||||   | || |   |||  |   | ||||||
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcag

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G142984_T01 (Zea mays), 5'ss of exon 3
--------------------------------TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacccacaactctgaagttattgtagtgcattattatttttttctg-ttctagaagattg--atcctgactaat--ggttgagagttacga---tattgcag
                                ||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||||||||||||||| || |||||||||||||||||||||||      | |    |  | ||    |||  | ||   ||||| |  || ||| ||||||  | | |||||||   | || |   |||  |   | ||||||
CTTGCATTCCCTGATGCTGTTTACCTAGTTGATGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTgtaagcccgcacttgagtctgatcatatcaccaaagttattcatgattgtaaaagggacagtgaggtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcag

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|27577389|gb|CB000084.1|CB000084
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|33795398|gb|CF323569.1|CF323569
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         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|218486574|gb|FG956238.1|FG956238
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTC
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTC
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|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|58655403|gb|CK044083.1|CK044083
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|27577933|gb|CB000628.1|CB000628
EST:     AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACCCTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
EST: gi|25801465|gb|CA757426.1|CA757426
EST:     AGTCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAG                         GCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG
genomic: AATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG

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: 43 (upstream exon), 68 (downstream exon)
Score: 328

TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacc ... gatattgcagGCTCTGTATTTCCAGTTTGGCATAAAATTGCATAATGTGATGGATACACAG




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