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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataataactggaggcatgacttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 6
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt--caacagtgtc-cataataactggaggcatgacttgtattcatcaa--gcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag
||||||||| ||||||||| |||| || |||||||||||||||||||| || || ||||||||||| || || |||||||||||||||||| |  ||  ||  | |||  ||| || ||||||| |||| |||  ||   | ||    || ||  | | |    ||||  |  ||||||   |||   | ||| |||
GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAGCTACGTTCATCTTTGTACACTCTACTGGTGGCTCAGgtaagacgttggcataattgttgcattattactggagacatggcttacatgatttaataaaataattattgttcggttagttgattctaactatatttacat-gtatcag

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 5
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtcca-taataactggaggcatgacttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag
 || ||||| ||||| ||||||||||||||| | ||||| |||||||| |||||||| || || || ||||| || ||||||||||||| |||| |  | || |  |   ||||  || |     | | |  | || |    | ||| || |   |  | |   ||||   | ||    |  || || |    
TGTATATGGCGAACCAATTCCTGTTAAGGAACTTGCTGACCGTGTGGCTAGTTATGTGCACCTCTGTACGCTATATTGGTGGCTCAGgttatatgtgaaccaattcctgctaatgtcttgtcttgt-agtcattttaaagttgtattgtcatatttcgtattaacaacag-atctataatggtgctgcag---

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G14330.1 (Glycine max), 5'ss of exon 5
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccat-aataactggaggcatgacttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag
 || ||||| ||||| ||||||||||||||| | ||||| |||||||| |||||||| || || || ||||| || ||||||||||||| |||| |  | || |  |  | |||  || |     | | |  | || |    | ||| || |   |  | |   ||||   | ||    |  || || |    
CGTATATGGCGAACCAATTCCTGTTAAGGAACTTGCTGACCGTGTGGCTAGTTATGTGCACCTCTGTACGCTATATTGGTGGCTCAGgttatatgtgaaccaattcctgttaatgtcttgtcttgt-agtcattttaaagttgtattgtcatatttcatattaacaacag-atctataatggtgctgcag---

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 5
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataataactggaggcatgacttgtattcatcaa-gcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag
 || ||||| ||  |  | ||||| |||||| |  |||| ||||| ||||||||||| ||||| || || ||||| |||||||||||||              ||||||    | ||     | |   | ||| ||| | | |||||   |   ||    |     |    ||   ||||| | || |     
TGTTTATGGCGATGCTGTACCTGTGAAGGAACTTTCTGAGCGTGTTGCAAGTTATGTACATCTGTGTACCCTGTATTGGTGGCTCAGgtt-------------tgtccaattcatcta----cgtctttggtagtcacctacgcatttctcctacttgaatgaattataagaaaatggtttttattttgtag-

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataata-actgg---aggcatg-acttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag-----------------------------------------------------------------------------------------
  | ||||| ||     ||||| |    ||| |   ||| ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   | |   |||  ||  |||||  |||     ||  | | | ||  ||   | |  ||   ||    |   | |  | || |    |  | |      | |||                                                                                            
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag

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|22819364|gb|BU499454.1|BU499454
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGT
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGT
EST: gi|91049728|gb|EB160146.1|EB160146
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|22491453|gb|BU051376.1|BU051376
EST:     ATCGTGTGGCAAGTTATGTTCATCTTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTTGGCTGCGGCGTTATTCTTGGAGGTTATGATAGGGATGGGCCAC
genomic: ATCGTGTGGCAAGTTATGTTCATC-TTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCC-TTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCAC
EST: gi|22819362|gb|BU499452.1|BU499452
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|78106192|gb|DV524610.1|DV524610
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|211064278|gb|FK983495.1|FK983495
EST:     GATCGCGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGT
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGT
EST: gi|93284361|gb|EB676625.1|EB676625
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|22819430|gb|BU499520.1|BU499520
EST:     ATCGTGTGGCAAGTTATGTTCACTCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGAGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: ATCGTGTGGCAAGTTATGTTCA-TCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|21843523|gb|BQ704104.1|BQ704104
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGCGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|50333782|gb|CO528908.1|CO528908
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|149084419|gb|EE173874.2|EE173874
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAG                         GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA
genomic: GATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatt ... gttgtaccagGCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataataactggaggcatgacttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG