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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctcatatcctcgatgttaatgaacataaattaatttaagggtgcctaaatgtgagtaacttatgtgattaaatcaccaatcttattatttaacag

Basic information

species Zea mays
transcript GRMZM2G060842_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060842_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g20640.1 (Oryza sativa), 5'ss of exon 5
CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctcatatcctcgatgttaatgaacataaattaatttaagggtgcctaaatgtgagtaacttatgtgattaaatcaccaatcttattatt-taacag-----
|| ||||||||| |  ||||| ||||| |||||| |||||| || || |||||||| |||||||| || || |||||||||||| ||    | ||  |  |  || || |      || || |||    |  ||   ||        | |   || ||| |      ||   ||||| |   ||     
CTTAAGGATGAACTATTGCTCCTGACCACAGGAATTGGAGCTGCGTGCAGTTTATACTGTCTCCTAGTCTTTTCTCTGGAGgtaaat----agatttttcaaatttataattg-gcatcaaattagacattactctttgccgacg-ttaaaacgactaagtagtt--tcgagttattgtggtagtgtga
















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|76280845|gb|DV020413.1|DV020413
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|50327397|gb|CO522523.1|CO522523
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|76280844|gb|DV020412.1|DV020412
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|91875732|gb|EB405689.1|EB405689
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|76912690|gb|DV164849.1|DV164849
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|101386086|gb|EB815086.1|EB815086
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|50323043|gb|CO518169.1|CO518169
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGCTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
EST: gi|50326968|gb|CO522094.1|CO522094
EST:     GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG                         ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG
genomic: GAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctc ... tatttaacagACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAGgtacatcctcatatcctcgatgttaatgaacataaattaatttaagggtgcctaaatgtgagtaacttatgtgattaaatcaccaatcttattatttaacag

- - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - -  GAGCAG