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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGAAACCAAAGGAAGGTGACAGTATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatcgttagatcgtctacctgactgcttctggaaccgctaatctctttgttctatttaacgctatgcttcacaatgacattttatattggagcc...

Basic information

species Zea mays
transcript GRMZM2G014116_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
AAAAGAAACCAAAGGAAGGTGACAGTATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc-------gttagatcgtctacctgactgcttctggaaccgctaatc-tctttgttctatttaacgctatgcttcacaatgacattttatattggagcc
|||||||||| || |||||||| | |||||||||||| || || ||||| || |||||||| || ||| |||||||| ||||||| ||||||||||||||||||||| ||       || |||     |        | |  ||   |  ||| |  | || |||  | |||| ||||  |       |  ||   ||||        
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata--------

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 6
AAAAGAAACCAAAGGAAGGTGACAGTATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatcgttagatcgtctacctgact-gcttctggaac-cgctaatctctttgttctatttaacgct--atgcttcacaatgacattttatattggagcc
| || || || || |||||||| | | ||||| | || ||||||||||||||||| || || | ||| ||||||||  ||||||| ||||| |||||||||||  | ||  |    | ||   | |   | |||| |  ||   |||      |  |   | || ||   |  ||| |   |  | ||||  | ||| ||    
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGCAGATATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgattctctacttgttgtcttattttgcttgttcaatatgctgcctggtagggggtgttaaaatgtggatgttgttctgttacatagt-tatcggt---
















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|211388540|gb|FL326080.1|FL326080
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|31355001|gb|CD439358.1|CD439358
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|7216589|gb|AW562711.1|AW562711
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         NTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGNTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|31355164|gb|CD439521.1|CD439521
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|211150172|gb|FL276377.1|FL276377
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|31355423|gb|CD439780.1|CD439780
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCC
EST: gi|14202839|gb|BG836516.1|BG836516
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGAWTCG                         TTATTA-TCTCACAACAATGATTACTTGGAA-TCTGCGGT-GTTACA
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACA
EST: gi|9953978|gb|BE640561.1|BE640561
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|31350034|gb|CD434391.1|CD434391
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTTACA-GG
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTT-ACAAGG
EST: gi|213188018|gb|FM188229.1|FM188229
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|26457612|gb|CA829195.1|CA829195
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|71448354|gb|DR829404.1|DR829404
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGGAATCTGCCCGTTGTAACA-GG
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCC-GTTGTTACAAGG
EST: gi|213183945|gb|FM195837.1|FM195837
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
EST: gi|31354458|gb|CD438815.1|CD438815
EST:     ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCG                         TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC
genomic: ATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatc ... ttcttcacagTTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGAAACCAAAGGAAGGTGACAGTATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTTCTAGAATTGAAGCGCGTCTACTACGAACTGATGATTCGgtatgtcatcgttagatcgtctacctgactgcttctggaaccgctaatctctttgttctatttaacgctatgcttcacaatgacattttatattggagcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC