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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagagggaagctggcgatgtttaaatttgattttaacctccattagcatatgcttgatgagacaatactcaaattcacatcactaactgtttggttacagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG

Basic information

species Oryza sativa
transcript LOC_Os08g33830.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33830.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G082174_T05 (Zea mays), 3'ss of exon 3
----------------------------gtaaagagggaagctggcgatgtttaaatttgattttaacctccattagcatatgcttgatgagacaat--actc----aaattcacatcac-taactgtttggtta-cagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG
                             |   |      | ||   ||| ||||| || ||| |    |  | |   ||    || || |  ||    || |     ||||   |||   |   ||||   ||| |||||||||||| ||||| || ||||||||||| | ||||||||| ||||| || |  |||
gtactagaaattggcatcagctaaagtcttgcggcttcctgttgataatgcttaaaatt-attatccttttaagtgctatgctatttattaaccatctaacccttgtgaattgtgatcctatttttgttcatttaacagGGATTACACCAATCCTTACCTTCCTGTGAACCAAACAGCAATTGAGGGGATTGTGCAG

upper sequence: LOC_Os08g33830.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 5
---------------------------gtaaagagggaagctggcgatgtttaaatttgattttaacctccattagcatatgcttgatgagacaatactcaaattcacatcacta-actgtttggtt------acagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG
                            |   |     |  ||   ||| |||||    ||| |    |  | |   ||    || || |  || |  ||   |    ||    | ||| ||| |||      ||||||||||||| ||||| || ||||||||||| | ||||||||| ||||| || |  |||
gtattagaaagtggcataagctaagtcttgcggcttccaattgataatgcttaaaagatattatctttttaagtgctatgctatttattaaccatttatcccttgtgaattgtgatactattttgttgatttaacagGGATTACACCAATCCTTACCTTCCTGTGAACCAAACAGCAATTGAGGGGATTGTGCAG

upper sequence: LOC_Os08g33830.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 5
gtaaagagggaagctggcgatgtttaaatttgattt---taacctccattagcatatgcttgatgagacaatactcaa-----attcacatcactaactgtttggtta--cagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG
              ||   || |||  |||||  |    || |    |||     |   | | |   |  ||  |||      ||  |      |   | ||   | |  |||||| ||||| |||||||| |||||||||||||| || ||||| |||||||| ||||||
-------------ttgtttattttttgatttggatgatatagcacaaatttatgaacagtggtttctatgatgttcacttgatatctatggttttgtttattcaatcatgcagGGACTACACAAATCCATACCTTCCTGTGAATCCTACTGCAATTGAGGGAATAGCACAG

upper sequence: LOC_Os08g33830.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------gtaaagagggaagctggcgatgtttaaatt--tgattttaacctccattagcat--atgcttgatg-agacaatactcaaattcacatcactaactgtttggttacagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG
                                                            || |    | |  ||  |   | | ||    || ||||  |||   |  || |  ||  |||| | || |  | ||  || | | ||   |   | ||||||  |||||| |||||||||||||||||||| |||  |||| ||||||| || || |  |  |||
gtactgggcatcgatgatgtcggctgccggcgtttttcagatcgtcttctgggcggagcatatatttcgcatttgcagcgctctgaaccggtgttttttccctgtctgggcttgaatagttgacgtagcctttccttgaaatta-atagttttatttttggtatcagGGACTACACGAATCCATATCTTCCGGTGGCTCCATCAGCAATTGATGGTAGTGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatgcttgatgagacaatactcaaattcacatcactaactgtttggttacagGGATTACACGAATCCATATCTTCCTGTGAATCCAACAGCAATCGAGGGAATCGCACAG
                                   cactaac  putative branch site (score: 1)
                       tcaaatt  TA-rich tract