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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaactgcagctttaatcctaattgccacatccttttccaataatggtatgcacattggtgtaaaattatgaagacggcacatgtttgtttcctaattggtactgtatcacccatgctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA

Basic information

species Oryza sativa
transcript LOC_Os03g02150.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 2
gtgaaaactgcagctttaatcctaattgccacatcc-ttttccaataatggtatgcaca---ttggtgtaaaattatgaagacggcacat---gtttgtttcctaattggtactgtatc-acccatgctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
||      | ||| | || |     ||  || |||  |||| |   |||||||| |  |   ||| |||| ||| || |||    |  |       ||||| ||||||| ||   | |  |  ||||||||||||||| || |||||||||||||||||| ||||||| ||||| |||||| || | ||||| |||||||||||| | ||||||||||| ||||| |||||||
gtatggcattcagttatagtatcctttatcatatcaattttgctcaaatggtattcttaaatttgatgtagaataatcaaggtttcttagtgaacctgtttactaattgctatcattttgatgcatgctgcagGTTGGTTATATTGTGACATCTTGCTTACTGAATGAGAATAACGATTTCTTAAGAATGGTAATAAATACAGTAAGGAATGACATAATCGGACGAAATGAGA

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 3
gtgaaaactgcagctttaatcctaattgccaca----tccttttccaataatggtatgcacattggtgtaaaattatgaagacggcacat---gtttgtttcctaattggtactgtatcacccatgctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
||  ||  | ||| | ||||     ||||||||    |  |  ||  ||  |  | |  |  ||| |||| ||| || |||    |  |       ||||| |||| ||  |  || | || |||||||||||||||||| |||||||||||||||||| ||||||| |||||||||||| || | ||||| |||||||||||| | ||||||||||| ||||| |||||||
gtataacattcagttataatatcctttgccacaggaattttgctcacatggtattcttaaatttgatgtagaatgatcaaggtttcttagtggagctgtttactaaatgcca--gtttaacgcatgctgcagGTTGGGTATATTGTGACATCTTGCTTACTGAATGAGAATAATGATTTCTTAAGAATGGTAATAAATACAGTAAGGAATGACATAATCGGACGAAATGAGA

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
gtgaaaactgcagctttaatcctaattgccacatccttttccaat--aatggtatgcacattggtgtaaaattatgaagacggcacatgtttgtttcctaattggtactgtatcacccatg-ctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
                     ||  |       | |  || || |  | |   |||   |   | | |||  | |  |||| |   |       |||     |  || ||   ||   ||| |||||||||||||||||||| |||||  | ||  | ||||||||| |||| || ||  || ||| |||||||||||| |||||||| || || || || ||||| |
---------------------ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatctatagactgtgaagaaggaattc-----taatattg--ccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------gtgaaaactgcagctttaatcctaattgccacatccttttccaataatg-gtatgcacattggtgtaaaattatgaagacggcacatgtttgtttcctaattggtactgtatcacccatg-ctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
                                                                         ||  |    ||||| ||         |  ||  ||||   | ||    || |  |   | | |||  | |  |||| |   |    |  |||     |  || ||   ||   ||| |||||||||||||||||||| |||||  | ||  | ||||||||| |||| || ||  || ||| |||||||||||| |||||||| || || || || ||||| |
gtattttgttctccttcatgacacctttttataatgatttgtttctctctctctctctctctctctctctctcaatatattactttattctggtgaagtatttcagtttcagttcatttacatacctagcagagaaaatatctatagactgtgaagaagtaattc-----taatattg--ccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaagacggcacatgtttgtttcctaattggtactgtatcacccatgctgcagGTTGGGTACATTGTGACATCTTGCTTATTGAATGAAAATAATGATTTCCTACGGATGGTTATAAATACAGTACGCAATGACATAATAGGACGGAATGAGA
                       tcctaat  putative branch site (score: 2)
                 tttgttt  TA-rich tract