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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaccttggatttttacgttaaagcatccagtttccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG

Basic information

species Oryza sativa
transcript LOC_Os01g35170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g35170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G154087_T01 (Zea mays), 3'ss of exon 5
gtaagctaccttggatttttacgttaaagcatccagtttccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG
||| | | ||| | ||    |  |    |||       || || || |      | | |||   |   |||      | |  | |||  |||| ||||||||||||||||||||||||||||||||  |  | ||    ||||| |||||||||||| ||||||||||||| ||||||
gtaggttgcctggcatccgaattt---ggcacttg--ctctttcttatcagtgcagtaatgtatcatcacttgaaattattctctttcaacagCTATTTTATGTTTGCAAATGCAACAGTGTCTTTTGAGAAAATCATATCGTCATACCCTGGTCCCTTGTCACTTGTTTCAATACTG

upper sequence: LOC_Os01g35170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G054378_T03 (Zea mays), 3'ss of exon 5
------gtaagctaccttggatttttacgttaaagcatccagtttccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG
      ||| | | ||| | ||    |  |    |||       || || || |      | | |||  ||   |||      | |  | |||  |||| |||||||||||||||||||||||  |||||||  |  | ||    ||||| |||||||||||||||||||||||||| ||||||
gtacgtgtaggttgcctggcatccgaattt---ggcacttg--ctctttcttatcagtgcagtaatgtagcatcacttgaaattattctctttcaacagCTATTTTATGTTTGCAAATGCAACGATGTCTTTTGAGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTG

upper sequence: LOC_Os01g35170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G054378_T06 (Zea mays), 3'ss of exon 5
gtaagctaccttggatttttacgttaaagcatccagtttccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG
||| | | ||| | ||    |  |    |||       || || || |      | | |||  ||   |||      | |  | |||  |||| |||||||||||||||||||||||  |||||||  |  | ||    ||||| |||||||||||||||||||||||||| ||||||
gtaggttgcctggcatccgaattt---ggcacttg--ctctttcttatcagtgcagtaatgtagcatcacttgaaattattctctttcaacagCTATTTTATGTTTGCAAATGCAACGATGTCTTTTGAGAAAATCATATCGTCATACCCTGGTCCCCTGTCACTTGTTTCAATACTG

upper sequence: LOC_Os01g35170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G154087_T02 (Zea mays), 3'ss of exon 5
gtaagctaccttggatttttacgttaaagcatccagtttccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG---------------
||| | | ||| | ||    |  |    |||       || || || |      | | |||   |   |||      | |  | |||  |||| ||||||||||||||||||||||||||||||||  |  | ||    ||||| |||||||||||| ||||||||||||| ||||||               
gtaggttgcctggcatccgaattt---ggcacttg--ctctttcttatcagtgcagtaatgtatcatcacttgaaattattctctttcaacagCTATTTTATGTTTGCAAATGCAACAGTGTCTTTTGAGAAAATCATATCGTCATACCCTGGTCCCTTGTCACTTGTTTCAATACTGGTGAGTGTAGCTGGG

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|58693195|gb|CK081882.1|CK081882
EST:     TTGGTGGAGCGGTCGCAGTTCTGGGTAACCGAGTTGGGGCTTAGGAATGT                         TTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTC
genomic: TTGGTGGAGCGGTCGCAGTTCTGGGTAACCGAGTTGGGGCTTAGGAATGTgtaagctacc ... ttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttttttcagaaaatgatgaggcgatactaagtggtttcatttttgcacagTTATTTTATGTTTGCAAATGCAACAGTGTCTTTCAACCAGATTGCGTCGTCGTACCCTGGTCCCCTGTCACTTGTTTCTATACTG
                                       tttcattttt  CT-rich tract
     ttttttcagaaaat  TA-rich tract