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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g57140.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 9
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttgaaatgct-atacgttttctgccagttttagctaatttctt-tttctgcgttaatgcag
|||||||||||||||||| |||||||||||||| |||||||||||||||||||||||| |  ||||||||| ||| ||| |||| || ||||||||||||||||||| |   ||||  |  || ||   | |||   ||||||| |  |  | || |  |    ||||||| | |||||||
TCTTCCATATGGGAACTCTGTTTTCTTCAGTGTTCGGAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTTTGGGGATCAACAAACGAGGGgtctgat-ctcgaccatgtaatggaagcttcatattctttctgctaagtaaaactgaccttgaatttctgcatgaatgcag

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G423861_T01 (Zea mays), 5'ss of exon 10
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttg-aaatgctatacgttttctgccagttttagctaatttctt-tttctgcgttaatgcag
|||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||| |  ||||||||| ||| ||||||||||| |||||||||||||||||||  || ||||   | || |||    |||   ||||||  |  |  | || || |    ||| ||| | |||||||
TCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATGATCCAATAGGATTGCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgat--ctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcag

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 11
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgat--gcctaaccacatgttgaa----atgctatacgtttt----ctgccagttttagctaat---ttctttttctgcgttaatgcag----------------------
 ||||| ||||| || || |||||||||| ||| || |||||||||||||| || ||||||||||||||  | || ||| ||||||| || ||| ||||||| |||       ||  ||  ||| ||    |   ||||   |||     | | | | |||   |||   || |  || |   |   |||                        
ACTTCCTTATGGAAATTCTGTTTTCTTCAATGTTCGCAAGATTGATGATCCTATTGGACTTTTACCTGGTCGGATAATTTTGGGAATTAATAAAAGAGGGgtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatag

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 14
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgat------gcctaaccacatgttgaa----atgctatac-gttttctgccagttttagctaatttctttttctgcgtt-aatgcag-------------------------
 ||||| ||||| || || |||||||||| ||| || |||||||||||||| || ||||| ||||||||  | || ||| ||||||| || ||| ||||||| |||           ||  ||  ||| ||    |   ||||  |||| ||   |   |||   ||        | ||| || |||   |                         
ACTTCCTTATGGAAATTCTGTTTTCTTCAATGTTCGCAAGATTGATGATCCTATTGGACTCTTACCTGGCCGGATAATTTTGGGAATTAATAAAAGAGGGgtatgactaaacaaaaaaataactagttaaactaaacattatatagtttactattacaattattaaaaaatgaactgtgcttttaattgtgttttttcttgatcaattggctatag

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 5'ss of exon 8
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttgaaatgctatacgtttt------ctgccagttttagctaatttctttttctgcgttaatgcag---------------------------
 || ||||| ||||| |||||||| || || || || ||||| |||||||| || || |||||||||||  |||||||| |||| || |||||||| ||||| |  |  | |   | ||||| | |   |||   |||       |||  | | ||   |    |     |||  |||  || |                            
ACTGCCATACGGGAATTCAGTTTTTTTTAGCGTACGCAAGATAGATGATCCGATCGGTCTTTTACCTGGGCGAATCATTTTGGGTATCAACAAACGTGGGgt-tagtctcaatataaatgtt-atacattatgactttaaaaaaactgttattgttgtttggaattcaaatctatgttgttggatttgaatttgttgtttgctttcttgtag

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 10
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacat-gttgaaatgctatacgttttctgccagttt--tagctaatttctttttctgcgttaatgcag---------------------------
 || || |||||||| || |||||||| ||||| || |||||||||||||| || |||||||| |||||| | |||||  |||| || || || ||||||||  ||  |  |   | ||  ||  |||| |||  ||    ||| | |||  |   | | || |   |||     ||   |                            
ACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATGATCCCATTGGACTTTTGCCTGGACGGATCATCTTGGGCATTAATAAGCGAGGGgt--gagtcagagttatattattataatg-tatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacag

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|58671897|gb|CK060583.1|CK060583
EST:     CAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGG                         GTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTG
genomic: CAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcc ... gttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATGATCCAATAGGACTTTTACCTGGAAGAATCATTCTGGGAATAAACAAACGAGGGgtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA