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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa...

Basic information

species Oryza sativa
transcript LOC_Os07g30840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 2
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaag--ggagcgtttagatccttggcaa
||||||||||    || || ||| |||| ||||| || ||||| ||||| ||||| ||||||||||||||| |||| |||||||| ||||||||||||  | |  |  || | ||||||     ||| |    | |  || |  |      |||  |   | || |   | |||  | |  |||  |||| 
GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattctgacgaagcctatttaatatttggagcaatcagctata-gcatgacaatgacacaagattatgcttatttgtagccatcacttcca-ggcat

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G115277_T02 (Zea mays), 5'ss of exon 3
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa----
                                      ||||| ||||| ||||||||||| ||||||||| |||| |||||||| ||||| ||||||  | | ||   |||||||||      ||| |  | | |  || |  ||  || ||| |||| || | |      ||    |||  | |||     
--------------------------------------GTCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacaaattctgacagaacttgtctaatacctggagcaatcatctgta-gcatg-ccaatg-acacaaagcta-tgattatttgtagctatcacttgcagccat

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G115277_T01 (Zea mays), 5'ss of exon 3
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa----
||||||| ||    || || |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||| |||| |||||||| ||||| ||||||  | | ||   |||||||||      ||| |  | | |  || |  ||  || ||| |||| || | |      ||    |||  | |||     
GTAATTCGGGATCCCTTCCAGCATTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacaaattctgacagaacttgtctaatacctggagcaatcatctgta-gcatg-ccaatg-acacaaagcta-tgattatttgtagctatcacttgcagccat

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G027551_T01 (Zea mays), 5'ss of exon 1
-----------GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa----
           ||||||| ||    || ||  ||||||| ||||| || ||||| ||||| ||||||||||| ||||||||| |||| |||||||| ||||| ||||||  | | ||   |||||||||      ||| |  | | |  || |  ||  || ||| |||| || | |      ||    |||  | |||     
TGCAAGTTTAGGTAATTCGGGATCCCTTCCAACATTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacaaattctgacagaacttgtctaatacctggagcaatcatctgta-gcatg-ccaatg-acacaaaggta-tgattatttgtagctatcagttgcagccat

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G152805_T01 (Zea mays), 5'ss of exon 3
-----GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa----
     ||||||| ||    || || |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||| |||  |||||||| ||||| ||||||  | | ||   |||||||||      ||| |  | | |  || |  ||  || ||| |||| |||  |      ||    |||  | |||     
TTTAGGTAATTCAGGATCCCTTCCAGCATTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGTAGAGTCAACTAAGgtacaaattctgacagaacttgtctaatacctggagcaatcatctgta-gcatg-ccaatg-acacaaagctac-gattatttgtagctatcacttgcagccat

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G085670_T03 (Zea mays), 5'ss of exon 3
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa----
 |||||| ||    || || |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||| |||| |||||||| ||||| | ||||  | | ||   |||||||||      ||| |  | | |  || |  ||  || ||| |||  || | |      ||    |||  | |||     
ATAATTCGGGATCCCTTCCAGCATTGTTGCCTGATCAGGTCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattctgacagaacttgtctaatacctggagcaatcatctgta-gcatg-ccaatg-acacaaaacta-tgattatttgtagctatcacttgcagccat

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|88363229|gb|CI643087.1|CI643087
EST:     TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAG                         GTGCTACCATATGATCAACTCATGCAAG
genomic: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaattt ... ttctattcagGTGCTACCATATGATCAACTCATGCAAG
EST: gi|86821685|gb|CI309190.1|CI309190
EST:     TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAG                         GTGCTGCCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGA
genomic: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaattt ... ttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaagggagcgtttagatccttggcaa

- - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggagcg