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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgtatcaaatctctcaaccttatcttctaaccttgcctcttgttatacagtgctctttatctgttatactcattatactaactcctttcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTATCAAATGCGGGTCTCCAAACTTCACAAATAGATTATTATGAGATAAACG

Basic information

species Oryza sativa
transcript LOC_Os01g02020.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G860137_T01 (Zea mays), 3'ss of exon 9
tcatgtatcaaatctctcaaccttatcttctaaccttgcctcttgttatacagtgctctt--tatc-tgttatactcattatactaactcctttcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTATCAAATGCGGGTCTCCAAACTTCACAAATAGATTATTATGAGATAAACG
  |||| |  |  ||     | ||| ||   || || || |  ||| | | |   | |     ||| | |||||     | | |   |||||| | |    ||||||||||  | ||||| ||  ||||||| ||||| |||||||||||| |||||||||| | ||| ||||||||||| ||||||||||||||  |||| |
-gatgtgttca--ctggagtcgttacctagaaatctcgcttactgtgacatatcacaccgagcatcattttatatctgctgtgcgccctccttgctaatgtagGCACCTGAGCTGTTTACGACAGCTCCAGCCCTTGCCATTCCAAAGGCTATATCAAATGCAGCTCTTCAAACTTCACAGATAGATTATTATGAAGTAAATG
















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|58609247|gb|CK037280.1|CK037280
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|29675317|gb|CB671592.1|CB671592
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|218504789|gb|FG958555.1|FG958555
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|29640751|gb|CB645758.1|CB645758
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|29641200|gb|CB646207.1|CB646207
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|66915792|gb|CX102640.1|CX102640
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
EST: gi|218480326|gb|FG963594.1|FG963594
EST:     TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG                         GCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA
genomic: TTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAGgtaactctta ... tcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacagtgctctttatctgttatactcattatactaactcctttcaagcacagGCACCTGAATTATTTACAACTACTCCAGCTCTTGCTATTCCAAAGGCTGTATCAAATGCGGGTCTCCAAACTTCACAAATAGATTATTATGAGATAAACG
                                 tactaac  putative branch site (score: 0)
                                       ctcctttc  CT-rich tract
                     ttatactcattata  TA-rich tract