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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataatactttgaccttaagcatcgattaaatattcaaacatgctgatgctctctattgctttgtaaaatatattgatatacatcagagaaagatgatatgcttatgctattttgagctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAG

Basic information

species Zea mays
transcript GRMZM2G055020_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 6
gtgataatactttgaccttaagcatcgattaaatattcaaacatgctgat-gctctcta---ttgctttgtaaaatat-attgatatacatcagagaaagatgatatg-------cttatgctattttgagctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAG
||||  |   |||||| ||||| ||   | |     |||   |||   ||  || | ||   |   ||| |  | | | ||  | ||  |    | ||   |   |||        || |  | | |||  | |||||||||| |||| |||||||||||||| || |||||||| ||||||||||||||||| ||||  || ||||| |||||||||||| || | || ||||||||||
gtgactactgtttgactttaagtatatgtcatcatatcagttatgtcaattactttgtaaaatctatttatgcattgtcatcaaaattaactttataagcttctcatgaaagagcttttttgtgtcttgtccaaactcagGGTGAGCTAACTTATGGGAAAATAGGGGAATGGCGGTTTGACAAAAGATCTTATCTTCGTTCACCACCGCCAAGAAATCTTACATTACCTCCTCCAGGAG
















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|5468725|gb|AI834516.1|AI834516
EST:     GCAACNCATTCATCATCCCTTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|71761576|gb|DR959513.1|DR959513
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|5895926|gb|AW037172.1|AW037172
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|74237664|gb|DT645578.1|DT645578
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|78082143|gb|DV510555.1|DV510555
EST:     ACAACACATTCATCATCCATTATACGTATGGATGGGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATGGGTGAATGGGGTTTTGACAAAAGATTT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|76015780|gb|DT942950.1|DT942950
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|5686756|gb|AI939849.1|AI939849
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|211541009|gb|FL454732.1|FL454732
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTATTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|76917228|gb|DV166719.1|DV166719
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|74245896|gb|DT653810.1|DT653810
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|71763634|gb|DR961571.1|DR961571
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATTT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|60347170|gb|DN214143.1|DN214143
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|78023550|gb|DV491937.1|DV491937
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|211218550|gb|FL110185.1|FL110185
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAA                         GGTCAGCTTACTTATGGGAAAA
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAA
EST: gi|113702992|gb|EE680496.1|EE680496
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|71760330|gb|DR958267.1|DR958267
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|60351853|gb|DN218826.1|DN218826
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|33094629|gb|CF054623.1|CF054623
EST:     ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
EST: gi|148981075|gb|EE027418.2|EE027418
EST:     ACAACACATTCTTCATCCATTATAGGTATGGATGGGATTATTCAATGAAG                         GGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT
genomic: ACAACACATTCATCATCCATTATACGTATGGATGCGATTATTCAATGAAGgtgataatac ... gctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatatacatcagagaaagatgatatgcttatgctattttgagctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAG
                                            agctaac  putative branch site (score: 2)
     atatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataatactttgaccttaagcatcgattaaatattcaaacatgctgatgctctctattgctttgtaaaatatattgatatacatcagagaaagatgatatgcttatgctattttgagctaactcagGGTCAGCTTACTTATGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAG

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