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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatttccattacatagttgtatcaacatgagtgcataggctcattgtgttagtttgaatatgaattatgtcttccatcagtcatgt...

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 7
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 7
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 7
GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatttccattacatagttgtatcaacatgagtgcataggctc-attgtgttagtttgaatatgaattatgtcttccatcagtcatgt
||||||||| || || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || || ||||| |   ||| || | | |  | |        ||  | |  |  | | |  |   || | ||  | |  || ||||  ||   |  ||       |||
GCCTTTTGGTTGTGGAGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATCGAACCCTCAGGAGTCTCATACgtaagctaacactacagtac-acaagaagtcaaactcgtcttaggctcttggtttttgtttttttcatctctatgtgaaccattattagcaattaaattgt

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA05G14330.2 (Glycine max), 5'ss of exon 6
GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatttccattacatagttgta----tcaacatgagtgcataggctcattgtgttagtttgaatatgaattatgtcttccatcagtcatgt-------------------------
 |||||||| || ||||| || || ||||||||||| |||||||| |||||| | |||||| | ||||| || || ||||| ||||| || |  |  |     |    ||   | ||  |    ||   || | | || | ||   |  | ||  |||    | |    ||||  |   |  || |||                          
ACCTTTTGGATGTGGTGTCATACTAGGAGGTTATGACAGGGATGGACCACAGTTGTACATGGTTGAACCTTCCGGTGTTTCCTATgtgagctactttttgtcatttgatagcaacttccagacttctttataattacacatgcaattgatattcctttttggaagttccatgtggtatttttgtaatgatttgttcatttggtaattgttctag

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 6
GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatt--tccattacatagttgta---tcaacatgagtgcataggctcattgtgttagtttgaatatgaattatgtcttccatcagtcatgt-------------------------
 |||||||| || ||||| || || ||||||||||| |||||||  |||||| | |||||| | ||||| || || ||||||||||| |||      |   ||  |  ||  ||   |  |    ||   || | | || | ||   |  | ||  |||    | |    ||||  |   |  || |||                          
ACCTTTTGGATGTGGTGTCATACTAGGAGGTTATGACAGGGATGAACCACAGTTGTACATGGTCGAACCTTCTGGTGTTTCTTATgtgagtatactttttgttatttgatagcaacttcctgacttccttataattacacatgcaattgctattccttttttgaagttccatgtgctatttttgtaatgatatgttcgtttggtaattgttctag

upper sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 6
GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatttccattacatagttgtatcaacatgagtgcataggctcattgtgttagtttgaatatgaattatgtcttccatcagtcatgt
|||||||||||| || ||||||||||||||||||||||| ||||| || ||  | |||||||| ||||| |||||  | || ||||||||||  | ||||   |  ||   ||   | | | |  ||||     || | |  || |    ||    ||||||||| |   ||||  |||      
GCCTTTTGGCTGTGGGGTTATTCTTGGAGGTTATGATAGAGATGGACCTCAATTGTACATGATTGAACCATCAGGCATATCATATgtaagttatttctgcccgtagat---atgtgtctttaagtatgaaattttacgttatttttccctgtcatcatatgaattcta--ttcctgcag------

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|91049728|gb|EB160146.1|EB160146
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|22491453|gb|BU051376.1|BU051376
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|22819362|gb|BU499452.1|BU499452
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTA
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTA
EST: gi|78106192|gb|DV524610.1|DV524610
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTTTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|6342734|gb|AW165558.1|AW165558
EST:     ATAGGGATGGGCCCCAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|93284361|gb|EB676625.1|EB676625
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
EST: gi|149084419|gb|EE173874.2|EE173874
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGG
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGG
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTAT                         AAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC
genomic: ATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggt ... acttgaacagAAATACTTTGGTGCTGCATTAGGGAAGGGGAGACAGGCTGCAAAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTTTGGCTGCGGTGTTATTCTTGGAGGTTATGATAGGGATGGGCCACAGCTCTACATGATAGAACCCTCAGGAGTTTCTTATgtaagttggtactgcatttccattacatagttgtatcaacatgagtgcataggctcattgtgttagtttgaatatgaattatgtcttccatcagtcatgt

- - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC