RetrogeneDB ID: retro_dnov_468

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5098:19569..20323(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSDNOG00000010907
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_dnov_468
GTGTACCAGAACCTCTACTGAAGAAGAAGCAGTACTGGAGCCACTGACATTAAGCTAGGCTAGCCCCACAATTTCACCAA
CATGTTAGGCTACCCCGATGCTCAGTTCACTGGGCTCATGCACATGTATCTCACCATCCACAGTGACCATGAGGGCAGCA
ATGTAAGTGCCCATACCAGCCATTTGGTGGGCAGTGCCCTTTCTGACCCCTGCCTGGTCTTTGCCACAGCCATGAATGGG
TTGATAAGGCCCCTACATGGACTGACAAATCAGGAAGTACTTGTATGACTGACACAACTACAAAAGGAAGTTGGCAAAGA
TACGTCAGATGAGAAATTAGGAGACTATATCTGGAACACACTCAGCTCAGGACCAGTTGTCCCAGACTACGGCCATGCTG
TATTAAGAAAGACTGATCCACGATAGGTCTGTCGGTGAGAGATTGCTCTGAAACACCTGCCTAAAGATCCCATGTTTAAG
CTGGTTGCTCAGTTGTACAAGATTGTGCCCAATGTTCTCTTAGAGCAGGACAAGGCCAAGAATCCCTGGCCCAATGTAGA
TGCTCATAGGGAAGTGCTGCTCCAGTTCTATGACATGATGGAGATGAATTACCACATGGTCCTGTTTGGAGTGTCACGAG
CACTGGGCGTACTGGCACAACTCATCAGCAGCTGAGCCCTAAGGTTTCCCTCTAGAGAGACCCAAGTCCATGAGCACGGA
TGGTCTGATGAAGTTTGTGGATTCTAAGTCAGGG

Alignment

ORF - retro_dnov_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.54 %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IYRNLYREGSSIGAIDTKLDWSHNFTNMLGYTDAQFTELMRMYLTIHSDHEGGNVSAHTSHLVGSALSDP
          .Y.NLY...SS.GA.D.KL...HNFTNMLGY.DAQFT.LM.MYLTIHSDHEG.NVSAHTSHLVGSALSDP
Retrocopy VYQNLY*RRSSTGATDIKLG*PHNFTNMLGYPDAQFTGLMHMYLTIHSDHEGSNVSAHTSHLVGSALSDP

Parental  YLAFSAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDP
          .L.F..AMNGL..PLHGL.NQEVLV.LTQLQKEVGKD.SDEKL.DYIWNTL.SG.VVP.YGHAVLRKTDP
Retrocopy CLVFATAMNGLIRPLHGLTNQEVLV*LTQLQKEVGKDTSDEKLGDYIWNTLSSGPVVPDYGHAVLRKTDP

Parental  RYVCQREFALKHLPNDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFG
          R.VC..E.ALKHLP.DPMFKLVAQLYKIVPNVLLEQ.KAKNPWPNVDAH..VLLQ.Y.M.EMNY..VLFG
Retrocopy R*VCR*EIALKHLPKDPMFKLVAQLYKIVPNVLLEQDKAKNPWPNVDAHREVLLQFYDMMEMNYHMVLFG

Parental  VSRALGVLAQLIWSRAL-GFPLERPKSMSTDGLMKFVDSKSG
          VSRALGVLAQLI.S.AL.GFPLERPKSMSTDGLMKFVDSKSG
Retrocopy VSRALGVLAQLISS*AL>GFPLERPKSMSTDGLMKFVDSKSG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	366.57 RPM
SRP012922_cerebellum	0.00 RPM	95.54 RPM
SRP012922_heart	0.00 RPM	271.71 RPM
SRP012922_kidney	0.00 RPM	95.55 RPM
SRP012922_liver	0.00 RPM	28.17 RPM
SRP012922_lung	0.15 RPM	60.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	313.80 RPM
SRP012922_spleen	0.00 RPM	75.66 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_468 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468 ,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,