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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaactgttgcaccatcacaaactaacaaatatttgattttaatatttattttattgttttattttttatgtctaagatgccaatgttgttaat...

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 5'ss of exon 6
ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaactgttg--------caccatcaca-aactaacaaatatttgattttaatatttattttattgttttattttttatg-tctaagatgccaatgttgttaat-----------------------------------------------------------------------------------------
| ||  |||||||||||||||||||||||||||||||||||||||||||||| ||  | ||||||||||| | ||||| ||| ||    |||          ||||  ||  || || | |  ||| ||| || |    ||  ||   |  || || | ||| |  ||||     || ||  || |                                                                                         
ACCCAACTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCACATTTGTTCCTCATTGGTAGAAGgtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagctatggttatctaaacag

upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 5'ss of exon 8
ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaactgttgcaccatc-acaaactaacaaatatttgattt--taatatttattttattgttttattttttatgtctaagatgccaatgttgttaat-------------------------------------------------------------------------
|||| ||||| |||||||||||||| ||  |||| |||||||||||||| || ||  | |||||  | |||| |||||        | ||  ||   || |    ||   |||| | | ||||  || | ||| ||||       | |  ||    | |   |      || | ||                                                                            
ATCCCGCTGCTAGTGCTGATCTAGCTGTAGTTCTAATGCAAGAAGGACTGGCACAAATCTTCCTTGTGGGCAGAAGgtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcag

upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 5'ss of exon 7
ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaactgtt----gcaccatcacaaactaacaaatatt-tgattttaatatttattttattgttttattttttatgtctaagatgccaatgttgttaat
|||||||||||||||||||| |||||||  || | |||||||||||| | || ||  |  |||||||||| | |||||  ||| |  ||       ||  ||  | || |      ||   ||| | |  |   |  | | |||    ||  || || ||||  |   |  | || |    
ATCCTGCTGCAAGTGCTGATTTAGCAGTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtagttgactaggacagaattcctaattggatcctaaggtgactcttgtgactggtgt-ttgcacaatagttaatctctacaagaacccttttat----

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|19351008|gb|BM895540.1|BM895540
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19272449|gb|BM888705.1|BM888705
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATA-CAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351610|gb|BM896142.1|BM896142
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351009|gb|BM895541.1|BM895541
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCGCCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|89251335|gb|DY623121.1|DY623121
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|22491504|gb|BU051427.1|BU051427
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGGCAT
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAA-CCCGGGCACGTATTGAAACATCAATTCCTAGGAAG-CAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTGCTGCAAGTGCTGATCTAGCAGTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaactgttgcaccatcacaaactaacaaatatttgattttaatatttattttattgttttattttttatgtctaagatgccaatgttgttaat

- - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAG