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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctggcatcctccactctatctgacaaacttctggtgtatgaccag

Basic information

species Oryza sativa
transcript LOC_Os01g53600.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G158562_T03 (Zea mays), 5'ss of exon 9
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctg----gcatcctccactctatctgacaaacttctggtgtatgaccag
||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||  | | |||| |  ||||  ||      |||  |   ||| || | ||| |  ||| |||| |||||||
GGCTGGGTGGCTTTTCGTCAAGGAGTGGAATGCGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgtaattgtaacatctgtctacttttatctttgccacatgttgtgctccatgttacagaaatctagtgtgtgaccag

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G158562_T04 (Zea mays), 5'ss of exon 10
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctg----gcatcctccactctatctgacaaacttctggtgtatgaccag
||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||  | | |||| |  ||||  ||      |||  |   ||| || | ||| |  ||| |           
GGCTGGGTGGCTTTTCGTCAAGGAGTGGAATGCGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgtaattgtaacatctgtctacttttatctttgccacatgttgtgctccatgttacagaaatctag-----------

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA06G19740.1 (Glycine max), 5'ss of exon 11
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctggcatcctccactctat---ctgacaaacttctggtgtatgaccag
|  |||| || ||| || |||||   |||||||||||| || ||  |||| ||||||||||| ||||| ||||| |||||||||||||| | ||  ||   |  ||||| ||        | ||      |||     ||   |    ||   | | | |||
GAATGGGCGGTATTCCGGCAAGGTAAGGAATGTGGATTCCAGGGGAGAACAAATAAATTGGTGGATGGATGCTATTCCTTTTGGCAGgtgattgaaat-tttactttttcttcatcaatcttctttgtgatatagttcgattgaaacttga-atgtaatcag

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G23780.1 (Glycine max), 5'ss of exon 11
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctggcatcctccactctat---ctgacaaacttctggtgtatgaccag
| |||||||| ||| || |||||   |||||||||||| || ||  |||| |||||| |||| ||||| ||||| |||||||||||||| | |   ||    || |||| ||        | ||      |||    |||   |    ||   | | | |||
GACTGGGTGGTATTCCGACAAGGTAAGGAATGTGGATTCCAGGGGAGAACAAATAAACTGGTGGATGGATGCTATTCCTTTTGGCAGgtgattaaaat-ttggtattttcttcttcaatcttctttgtgatatagtttgattgaaacttga-atgtaatcag

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G40280.1 (Arabidopsis thaliana), 5'ss of exon 11
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctggcatcctccactctatctgacaaacttctggtgtatgaccag------------------------
   ||||  | |  ||| |||||||| |||   |||||||||||  | || || |||||||| |||||||||||| | ||||||||||||||     || || |     || |  | |   |  |  ||  ||    ||   || | || | |    |                         
AATTGGGCTGTACATCGACAAGGAGTAGAAATGGGATTTCAAGGTAGGACGAACAAATTGGTCGATGGTTGCTACACATTTTGGCAGgttaactttctatctttcaggattattattggccctacttctaaattcttcaccgttgttgtcttttcttatttcctttgggtatatgttaaacag

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv14s0066g01310.t01 (Vitis vinifera), 5'ss of exon 11
GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgccatacctgttttttttttcctggcatcctccactctatctgacaaacttctggt-----gtatgaccag
|  ||||||| |||||| ||||| || ||  |||| || || ||  |||| ||||||||||||||||||||||| |||||||||||||| | |  |||   | |||      || |   ||  |    | |   | | |      |          ||||||||
GATTGGGTGGTATTTCGACAAGGTGTTGAGGGTGGTTTCCAGGGCAGAACCAATAAATTGGTTGATGGTTGCTATTCCTTTTGGCAGgtgattttcat-tttctttaccccatcatattattattgcttttgattaatagtggattaaataaaaaaatgaccag

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|218480035|gb|FG968183.1|FG968183
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|22306108|gb|BQ907330.1|BQ907330
EST:     TCAAGGCCGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCACG                         GGAGCTGCTCTTGCTTTAACACCAAAACTAATGACACGTTGTTGATGAGC
genomic: TCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCA-Ggttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACA-GTTGTTGATGAGC
EST: gi|29674619|gb|CB670894.1|CB670894
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29645257|gb|CB650264.1|CB650264
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29674661|gb|CB670936.1|CB670936
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29674660|gb|CB670935.1|CB670935
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29674620|gb|CB670895.1|CB670895
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29645420|gb|CB650427.1|CB650427
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29640149|gb|CB645158.1|CB645158
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29661886|gb|CB658161.1|CB658161
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 36 (upstream exon), 65 (downstream exon)
Score: 13

GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG




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