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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatcctgtctatgaaatatcttatattttcatttttttactatgttgacttcatttaatatattttaaatccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT

Basic information

species Zea mays
transcript GRMZM2G402242_T02
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 6
-----atatcctgtctatgaaatatcttatattttcatttttt-tactatgttgacttcatttaatatattttaa-atccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
     |||||||   |||| ||||||  |||| |||   | |  |  |||| |   || ||  | | ||| |||  |||||| ||   |||||||||||||||| |||||||||||||| ||||| ||||||||||
gttatatatccttattatgcaatatcccatatattctcatgtgatcttatgctctatttatcaattgtatgttattatccttgaccctatgacacgtatgcatatttcaaaaagCTGGACTACTTCTCCACAGAAT

upper sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
atatcctgtctatgaaatatcttatattttcatttttttactatgttgacttcatttaatatattttaa-------atccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
|||||||  ||||| ||||||  ||||    | | |  || |||| |   |||||  | |  | ||| |       |||||| ||   |||||||||||||||| |||||||||||||| ||||| ||||||||||
atatccttactatgcaatatcccatat----aatgtgatattatgctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT

upper sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 6
atatcctgtctatgaaatatcttatattttcatttttttactatgttgacttcatttaatatattttaaatccttaactgcatg-acacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
          | ||    |  || |  ||  || || ||   ||  | | ||| ||   ||   |  ||| ||||||| | ||  ||||||||||||| ||||||| ||| || ||||||||||| ||||
--------gttgtggttgagttttttgttatatgttattcagattattatttctttctgtaagCTGCAAAACCTTAACCGGATTTACACGTATGCATATTTCAAAAGGCTAGACTACTTTTCCACCGAAT

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|71774415|gb|DR972293.1|DR972293
EST:     ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT                         GTATGCATACTTCAAAAAGCTGGATTACTTTTTCACAGA
genomic: ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTATatatcctgtc ... tgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGA
EST: gi|71770543|gb|DR968480.1|DR968480
EST:     ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT                         GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
genomic: ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTATatatcctgtc ... tgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
EST: gi|91872707|gb|EB402664.1|EB402664
EST:     ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT                         GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
genomic: ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTATatatcctgtc ... tgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
EST: gi|50323940|gb|CO519066.1|CO519066
EST:     ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT                         GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
genomic: ATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTATatatcctgtc ... tgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttactatgttgacttcatttaatatattttaaatccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
 atccttaac  putative branch site 
        tatgttgacttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcctgtctatgaaatatcttatattttcatttttttactatgttgacttcatttaatatattttaaatccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA