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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatacttgattacctttttgccatcacatcctggattcccagttttcatactatttgtgtttgctgtactctacatgtttcaagggtctgtcttgcagttgcaggctttacaacctttcctattctgttgtttcag

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
CTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatacttg---attacctttttgccatcacatcctgga-ttcccagttttcatactatttgtgtttgctgtactctacatgtttcaagggtctgtcttgcagttgcaggctttacaacctttcc-tattctgttgtttcag
|||||||||   ||||| ||| ||||||||||||| ||||| |  ||||||||||||||||||| |||||| || |||||||||||||||||||| ||  ||| ||| |||     | || | |  |    ||||    |  |||  | || || | |   |     ||||       |   | |||  |    |||||||    ||| |   |||| ||  |  || | ||  |   ||||||
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcc---tcttgtgtattttcaattgctgtctt----ttgaaatttttagaatataaccatctttcgccatttcag
















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|60355106|gb|DN222079.1|DN222079
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|211389068|gb|FL236600.1|FL236600
EST:     AAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: AAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|148948633|gb|EC898545.2|EC898545
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|211389067|gb|FL236599.1|FL236599
EST:     AAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: AAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|213173207|gb|FM183700.1|FM183700
EST:     CGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAATCTCAACCCGAATCCTG
genomic: CGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|18179321|gb|BM380531.1|BM380531
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|8318714|gb|BE025279.1|BE025279
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
EST: gi|211035627|gb|FL437931.1|FL437931
EST:     GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttgtttcagTGGATTACCTCCTGTTCATGGTTCGTGACGTGAAGCTCAACCCGAATCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGGAATAGTTGCTGACGAATTACCTGTTGACCAGTTCATCCTCCTTGGGAGGATGCTTTACATGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatacttgattacctttttgccatcacatcctggattcccagttttcatactatttgtgtttgctgtactctacatgtttcaagggtctgtcttgcagttgcaggctttacaacctttcctattctgttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA