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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatatttcctttttatattgatatgtcaatcattctcacgacacttcttttgttgtcatataaccattggactatcaatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA

Basic information

species Oryza sativa
transcript LOC_Os05g01060.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 16
gtatgttatatttcctttttatattgatatgtcaatcattctcacgacacttctttt-gttgtcatataaccattggactatcaa----tcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA
||||||      | ||| | | || | | | ||||     |||     |  |||||   || |||||| ||| |  ||  |||||    |  |||||||||| ||| |||||||||||||||||||| | ||||||||||||||||||||||||||| ||||||||||||| ||||| ||||| ||| | |  || |
gtatgtccccaattcttctcaaat-ggtctttcaagagcactctttctatgtctttccattatcatatgaccctgtgaacatcaaattattctgcagGTTAGATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGA

upper sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
-----------------------------------------gtatgttatatttcctttttatattgatatgtcaatcat----tctcacgacacttcttttgttgtcatataaccattggactatcaatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA
                                         ||   |  | |||   | | | | |  |||    | |||    | |    |     | ||  |    |  | | | |    || | ||| ||||||| | | | ||| ||||| ||||||||||||   ||||| || |||||||||||||||||||| ||||||| ||| |   |||||| |||  |  | || |
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
















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|86479064|gb|CI121697.1|CI121697
EST:     TCAAGAAAATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCT                         GTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
genomic: TCAAGAAAATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCTgtatgttata ... aatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
EST: gi|218494468|gb|FG943637.1|FG943637
EST:     TCAAGAAAATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCT                         GTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
genomic: TCAAGAAAATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCTgtatgttata ... aatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
EST: gi|87014168|gb|CI273358.1|CI273358
EST:     CTATGAAGTTCTGCTGCCT                         GTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
genomic: CTATGAAGTTCTGCTGCCTgtatgttata ... aatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
EST: gi|86599676|gb|CI253661.1|CI253661
EST:     ATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCT                         GTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA
genomic: ATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCTgtatgttata ... aatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcacgacacttcttttgttgtcatataaccattggactatcaatcttgcagGTTAGGTTTCTAGATATGTGGGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAA
                        tcatataa  TA-rich tract