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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatgccatacctgttttttttttcctggcatcctccactctatctgacaaacttctggtgtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g53600.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G158562_T04 (Zea mays), 3'ss of exon 10
gttaatgccatacctgttttttttttcctg----gcatcctccactctatctgacaaacttctggtgtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG
|| | ||  | | |||| |  ||||  ||      |||  |   ||| || | ||| |  ||| |||| |||||||||||||||  ||||||| ||||||||  |||| ||  |||||||| ||||||| || || || |||||| ||||||||||  |||||||           
gtaattgtaacatctgtctacttttatctttgccacatgttgtgctccatgttacagaaatctagTGTGTGACCAGGGAGCTGCCATTGCTTTCACACAAAAGTTAATTACGATTGTTGATAAGCAATTGAAGTCCTCGTATTCCTGCAAAAGGCCATCAGGAGA-----------

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G158562_T03 (Zea mays), 3'ss of exon 9
gttaatgccatacctgttttttttttcctg----gcatcctccactctatctgacaaacttctggtgtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG
|| | ||  | | |||| |  ||||  ||      |||  |   ||| || | ||| |  ||| |||| |||||||||||||||  ||||||| ||||||||  |||| ||  |||||||| ||||||| || || || |||||| ||||||||||  ||||||| ||||| ||  
gtaattgtaacatctgtctacttttatctttgccacatgttgtgctccatgttacagaaatctagtgtgtgaccagGGAGCTGCCATTGCTTTCACACAAAAGTTAATTACGATTGTTGATAAGCAATTGAAGTCCTCGTATTCCTGCAAAAGGCCATCAGGAGAGGATGCCTGCA
















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|29674660|gb|CB670935.1|CB670935
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
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|29645257|gb|CB650264.1|CB650264
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29674619|gb|CB670894.1|CB670894
EST:     TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG                         GGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
genomic: TTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAGgttaatgcca ... gtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAA
EST: gi|29674661|gb|CB670936.1|CB670936
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttcctggcatcctccactctatctgacaaacttctggtgtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG
                           atctgac  putative branch site (score: 3)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatgccatacctgttttttttttcctggcatcctccactctatctgacaaacttctggtgtatgaccagGGAGCTGCTCTTGCTTTAACACAAAAACTAATGACAGTTGTTGATGAGCAATTAAAATCATCATATTCCAGCAAAAGGCCTCCAGGAGATGATGCTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG