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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccgcccgcagtatatagcttcagtttattggtcgatggagagcatattctccaacgaccgagtggcgtgtggatccgtctaacctcgcttgttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGGGCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG

Basic information

species Zea mays
transcript GRMZM5G898290_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G898290_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g36880.4 (Oryza sativa), 3'ss of exon 2
gtgccgcccgcagtatatagcttcagtttattggtcgatggagagcatattctccaacgaccgagtggcgtgtggatccgtctaacctcgcttgttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGAC---GAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGG-GCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG
                                            | |  | |   | ||      |||    || |  ||       |||  ||| |  | |   |||  ||  |||  |  ||   |   ||||||||| |  ||||||    ||||||||||||||||||||||||||||||||| |||||| | ||||| | | || |   | ||||| | |  | | || ||||  ||  |  ||   
--------------------------------------------gtacgtacgtgagcgttgatttggt---tgcacgcgcgcgcgttcgtgtgtgc--catgtcgcgatctgatgggtg-gtctggt---tggttgggtgca-gcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAG-GCGCGGGCGCGGGGACGG---

upper sequence: GRMZM5G898290_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g36880.2 (Oryza sativa), 3'ss of exon 2
gtgccgcccgcagtatatagcttcagtttattggtcgatggagagcatattctccaacgaccgagtggcgtgtggatccgtctaacctcgcttgttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGAC---GAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGG-GCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG
                                            | |  | |   | ||      |||    || |  ||       |||  ||| |  | |   |||  ||  |||  |  ||   |   ||||||||| |  ||||||    ||||||||||||||||||||||||||||||||| |||||| | ||||| | | || |   | ||||| | |  | | || ||||  ||  |       
--------------------------------------------gtacgtacgtgagcgttgatttggt---tgcacgcgcgcgcgttcgtgtgtgc--catgtcgcgatctgatgggtg-gtctggt---tggttgggtgca-gCAGGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAG-GCGCGGGCGCGGGGA------
















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|78085883|gb|DV514276.1|DV514276
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|71441853|gb|DR822903.1|DR822903
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|71317486|gb|DR795459.1|DR795459
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|149080827|gb|EE169898.2|EE169898
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|78075643|gb|DV504077.1|DV504077
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|148990310|gb|EE031912.2|EE031912
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|76287206|gb|DV026774.1|DV026774
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|149108650|gb|EE292890.2|EE292890
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCTGTCAGAGCTGGCGCGTCCAAG                         GACGAGTGGGTGCTGTGCAGG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGG
EST: gi|149071005|gb|EE159410.2|EE159410
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|89759018|gb|DY687976.1|DY687976
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|74232934|gb|DT640848.1|DT640848
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|149088337|gb|EE177434.2|EE177434
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
EST: gi|78080430|gb|DV508842.1|DV508842
EST:     CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAG                         GACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG
genomic: CCAGCAGCAGCCGCCTCATGCCGTCGTCGGTCAGAGCTGGCGCGTCAAAGgtgccgcccg ... gtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGGGCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG
     tctttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccgcccgcagtatatagcttcagtttattggtcgatggagagcatattctccaacgaccgagtggcgtgtggatccgtctaacctcgcttgttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGGGCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG