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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctatttgttttgcagtttgatttcaatcacttaggggatcatatttttctctgtaactcataatatgtactagtggtgcagcatattcttataggttatgctttgtagtttggattcaaacaaattcaatgcttgcattctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA

Basic information

species Oryza sativa
transcript LOC_Os04g04020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g04020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143725_T01 (Zea mays), 3'ss of exon 4
gtatgtgctatttgttttgcagtttgatttcaatcacttaggggatcatatttttctctgtaactcataatatgtactagtggtgcagcatattcttataggttatgctttgtagtttggattcaaacaaattcaatgcttgcattctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA
                                          | ||| | ||| ||| |||   | ||  | | | ||    ||||  ||| || ||||   |||| | ||  | |   || ||| | || | |      |  ||||||| || |||||||||||||||| ||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||
------------------------------------------gtatcgtttttatctgtgtttttaatttttttttctga--gtgc--catctttttatt--ttatccctt--aat---gactcacataattactgccact-tattcttttagATTGTTGCAAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATA

upper sequence: LOC_Os04g04020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G874869_T01 (Zea mays), 3'ss of exon 4
gtatgtgctatttgttttgcagtttgatttcaatcacttaggggatcatatttttctctgtaactcataatatgtactagtggtgcagcatattcttataggttatgctttgtagtttggattcaaacaaattcaatgcttgcattctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA
                                                           |||   |   || | |  |    | ||  ||| || ||| |  || | |||  |   |   |||   ||          |||  ||| ||| ||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| |||||||
-----------------------------------------------------------gtatggctccatcttttttttctgagcgccatctttttaaa--ttttccttaatgactcacattattac-----tgccactt--atttttttagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGAACTTCCAGGCTTTCCACGAACACAGATTGGATTCTTAACCTTTGACAGCACCTTGCATTTTCATA
















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|29633800|gb|CB638809.1|CB638809
EST:     TCGAAGCGGGCTGCTTGAG                         GTTGTTGCAAAAACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
genomic: TCGAAGCGGGCTGCTTGAGgtatgtgcta ... attctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
EST: gi|88588495|gb|CI706315.1|CI706315
EST:     TCTTTCTTATTGATGTGTCCGTATCTGCAGTTCGAAGCGGGCTGCTTGAG                         GTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
genomic: TCTTTCTTATTGATGTGTCCGTATCTGCAGTTCGAAGCGGGCTGCTTGAGgtatgtgcta ... attctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
EST: gi|29633801|gb|CB638810.1|CB638810
EST:     TCGAAGCGGGCTGCTTGAG                         GTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
genomic: TCGAAGCGGGCTGCTTGAGgtatgtgcta ... attctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
EST: gi|426130|gb|D21986.1|D21986
EST:     GCAGTTCGAAGCGGGCTGCTTGAG                         GTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA
genomic: GCAGTTCGAAGCGGGCTGCTTGAGgtatgtgcta ... attctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCA

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: 73 (upstream exon), 72 (downstream exon)
Score: 35

TGTTGCTCCCACTGAATATATGGTGCGGCCACCAATGCCACCCTCCTATTTCTTTCTTATTGATGTGTCCGTATCTGCAGTTCGAAGCGGGCTGCTTGAGgtatgtgcta ... attctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggttatgctttgtagtttggattcaaacaaattcaatgcttgcattctttcagGTTGTTGCAAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATA
                                            cattctttc  CT-rich tract
                          aaacaaatt  TA-rich tract