RetrogeneDB ID:

retro_dnov_2616

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_90959:3660..4076(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000009992
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CDV3
Ensembl ID:ENSDNOG00000010208
Aliases:None
Description:CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]


Retrocopy-Parental alignment summary:






>retro_dnov_2616
CCAGGTGATAACTGGGAAGAAGATGGAGGTGGTGGTGGTGGTGTAGAAAATCTTCAGGTCCGTGGAATAAAACAGCTGTG
GTACAAGCACCTCCTGCTCCAGTAATTGTTACAGAAACCCCAGAACCGGCGATGACTAGTGGTGTGTATAGGCCTCCTGG
GGCCCGGTTAACCACAACAAGGAAAACACCACAAGGACCACCAGAGATATACAGCGATACACAGTTCCCGTCCCTGCAGT
CCACTGCCAAGCATGCAGAAAGCCGGAAGGATAAAGAAATGGAGAAGAGCTTTGAAGTAGTAAGACACAAAAATAGAGGT
AGGGATGAGGTTCCAAAAAACCAGGCCCTTAAACTTCAGCTAGACAACCAGTATGCTGTGCTTGAAAATCAGAAAAGCAG
CCACACACAGTACAGT

ORF - retro_dnov_2616 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.86 %
Parental protein coverage: 78.09 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalPGDNWEEGGGGGGGVE-KSSGPWNKTAVVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPE
PGDNWEE.GGGGGGVE.KSSGPWNKTAVVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPE
RetrocopyPGDNWEEDGGGGGGVE<KSSGPWNKTAVVQAPPAPVIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPE
ParentalIYSDTQFPSLQSTAKHAESRKDKEMEKSFEVVRHKNRGRDEVPKNQALKLQLDNQYAVLENQKSSHTQYN
IYSDTQFPSLQSTAKHAESRKDKEMEKSFEVVRHKNRGRDEVPKNQALKLQLDNQYAVLENQKSSHTQY.
RetrocopyIYSDTQFPSLQSTAKHAESRKDKEMEKSFEVVRHKNRGRDEVPKNQALKLQLDNQYAVLENQKSSHTQYS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 5 .45 RPM 26 .64 RPM
SRP012922_cerebellum 2 .75 RPM 13 .47 RPM
SRP012922_heart 9 .05 RPM 38 .29 RPM
SRP012922_kidney 7 .94 RPM 30 .67 RPM
SRP012922_liver 5 .42 RPM 20 .28 RPM
SRP012922_lung 4 .28 RPM 23 .67 RPM
SRP012922_quadricep_muscle 15 .40 RPM 48 .46 RPM
SRP012922_spleen 7 .44 RPM 33 .88 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_2616 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000355561 retrocopy
retro_btau_253,
Choloepus hoffmanni ENSCHOG000000089635 retrocopies
retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus ENSCJAG000000029981 retrocopy
retro_cjac_2928,
Dasypus novemcinctus ENSDNOG00000010208 5 retrocopies
retro_dnov_2359, retro_dnov_2616 , retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus ENSECAG000000156892 retrocopies
retro_ecab_444, retro_ecab_636,
Homo sapiens ENSG000000915271 retrocopy
retro_hsap_2678,
Gorilla gorilla ENSGGOG000000278211 retrocopy
retro_ggor_1869,
Myotis lucifugus ENSMLUG000000098641 retrocopy
retro_mluc_1296,
Mus musculus ENSMUSG0000003280310 retrocopies
retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys ENSNLEG000000034701 retrocopy
retro_nleu_1181,
Oryctolagus cuniculus ENSOCUG000000127481 retrocopy
retro_ocun_1106,
Ochotona princeps ENSOPRG000000036003 retrocopies
retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii ENSPPYG000000258981 retrocopy
retro_pabe_2301,
Pan troglodytes ENSPTRG000000154091 retrocopy
retro_ptro_1805,
Sus scrofa ENSSSCG000000116371 retrocopy
retro_sscr_701,
Tupaia belangeri ENSTBEG000000149105 retrocopies
retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta ENSTSYG000000114012 retrocopies
retro_tsyr_1381, retro_tsyr_1759,


Copyright © RetrogeneDB 2014-2017