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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGAGAAACTTCGCATGGGACAGCTAAACTGCAGAGATGAGGTGGTCGTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctctttagcccttggtcaaacacttctgattctgattttatcccctctaaaaagtattattcttaatatcttactcttgcag

Basic information

species Zea mays
transcript GRMZM2G154574_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154574_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g33100.1 (Oryza sativa), 5'ss of exon 7
GTTCAGAGAAACTTCGCATGGGACAGCTAAACTGCAGAGATGAGGTGGTCGTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattct---ctttagcccttggtcaaacacttctgattctgattttatcccctctaaaaagtattattcttaatatcttactcttgcag
| || ||||| |||||||||||  ||||  | || || ||||| ||||| ||||| |||||||| || |||||||| |||||||| |||||||||||||||||  || |   |  ||||||||||| ||   || || | | | | |   |    |   ||||  | | |||       | |  | ||  ||
GGTCTGAGAAGCTTCGCATGGGGAAGCTTGATTGTAGGGATGAAGTGGTGGTGGACTTGTTTGCAGGGATTGGATACTTTGTTCTACCATTTCTTGTGAAgtatgttatatacgatagcccttggttaa---ctgctaaatgttaataagtgattttacaaaataagtgttc-------cctttttttatag

upper sequence: GRMZM2G154574_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT4G04670.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCAGAGAAACTTCGCATGGGACAGCTAAACTGCAGAGATGAGGTGGTCGTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctctttagcccttggtcaaac-acttctgattctgattttatcccctctaaaa--agtattattcttaatatcttactcttgcag------------------------
  ||||| || ||||| |||||  |  |   |||   | |||| || ||||||||  |||||||||||||||||||||||||||| ||||||||||||| ||| || |  ||      |||   |||| |     ||   || |||||| |  || |||   | || | |  |  ||  | | |   | ||                         
TCTCAGAAAAGCTTCGTATGGGTAACATGGCCTGTGAAAATGAAGTTGTCGTGGACCTGTTTGCTGGAATTGGATATTTTGTTCTCCCATTTCTTGTGAGgtatatgccatt-----attgaataaacgagaagagaaagtggttttatacaatcaaaagtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacag
















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|87155467|gb|DY400256.1|DY400256
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|26559427|gb|CA831662.1|CA831662
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|26559057|gb|CA831292.1|CA831292
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|22542262|gb|BU092700.1|BU092700
EST:     G-GGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|32942516|gb|CF047335.1|CF047335
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|87155759|gb|DY400548.1|DY400548
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
EST: gi|22935761|gb|BU572036.1|BU572036
EST:     GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAA                         GGCTAATGCCAAGCTATTTTATGCATGTGAGTGGAATCCACATGCTCTGGA
genomic: GTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctc ... actcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGAGAAACTTCGCATGGGACAGCTAAACTGCAGAGATGAGGTGGTCGTGGATTTGTTTGCTGGAATTGGATATTTTGTTCTTCCATTTCTTGTGAAgtacattctctttagcccttggtcaaacacttctgattctgattttatcccctctaaaaagtattattcttaatatcttactcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA