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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG

Basic information

species Zea mays
transcript GRMZM5G840582_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 8
gtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG
                                                        |   |  || ||||   ||   |||   || ||  || |||| ||||| ||| | |||| |||||||||| |||  ||   |   | |||  ||||   || | ||||||||||||  | ||||||||||||||||| |||||||||||||| || | ||||||  |||| |||||
--------------------------------------------------------tagttcctgaaacagtttag--ttg---caactgtactaatt-ttcttgaagttatgttactttgctttaacaagttaataaaaatggtt--ttaa---tgtcatttacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG
















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|32942724|gb|CF047543.1|CF047543
EST:     ACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|32807630|gb|CD959864.1|CD959864
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTA
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTA
EST: gi|7216933|gb|AW563070.1|AW563070
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATAC
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATAC
EST: gi|32845230|gb|CD984911.1|CD984911
EST:     TACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: TACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG
                                         tctgcctttt  CT-rich tract
                                               ttttaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT