RetrogeneDB ID: retro_dnov_2013

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_42127:12013..12855(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSDNOG00000007807
• Aliases: None
• Description: forty-two-three domain containing 1 [Source:HGNC Symbol;Acc:25407]

Sequence

>retro_dnov_2013
ATGAACCGATTTGGTACCCGGTTGGTGGGAGACACGTTGGCTCTGTGGCCACCACCAAAAACCTGCAGCACAGAAAAGCT
AGGCAAAATTAATACGTCTTTGGATGATATAATCAAATTGAATTGAAAGGAAGGAAAGAAGCAGAATTCCCCAAGATTAA
ATAGACGACTCCAACAAAGTGGTACCCAGCAATTCAGGATGAGAATATCATGGGGAATCTGACAGAATTCTGGCTTTGAT
AAGAATAGTCTGAGCTGTAGAGTCATGCCTGGAAAGAGACGTCCTTACGGAGTTGTCACTGGCCTTGCAGCTAGGAAAGC
AGCCAGAATTCAAAAGGGAATGAGTCCCACGAATCGACTACCTCTAGGTGACAAGAATAGAGAGTGATATTTTCCTGTGT
TAAAAAGGAAGGCAAACCTTTTGAGACAAAATGAAGTGCAGAGGAAACCATAGCTGTTCTCAAGAAACCTAATCAGTAAA
ATGGAAAAAATAACATTCCAGTCAATTTTACCAGAAGTGGAAATAAATTAAGCCATCAGAAAGACATACATCAGGCAACT
TTTATTTTCAGAAGAGGCCTGAAGGTTCAGGCCCAGTTGAACACAGAACAACTACTAGATGACGTAGTAGCAAAGAGAAC
TCGTCAATGGTGGACTTCCACCACAAATGGAGGAATTTCATCTATACACACTGACAATCCTGGAGCGTGCAGTCCTCTGT
GACACAGAAACTGTGCTTAACTCAGCCTGTTGTGCCCTCATTCTTGACAATCAGGAGCAATCTGACATAAAGTAATTCCT
AAAGGTGTACCCCTACAATTTGACATAAATAGTGTTGAAAAA

Alignment

ORF - retro_dnov_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNRFGTRLVGATAAPALPTKTRSNENLDKIDMSLDDIIK-NRKEGKKQNFPRLNRRLQQSGTRQFRMRIR
          MNRFGTRLVG.T.A...P.KT.S.E.L.KI..SLDDIIK.N.KEGKKQN.PRLNRRLQQSGT.QFRMRI.
Retrocopy MNRFGTRLVGDTLALWPPPKTCSTEKLGKINTSLDDIIKLN*KEGKKQNSPRLNRRLQQSGTQQFRMRIS

Parental  WGIQQNSGFGKNNLGRRGRIMPGKRRPYGVITGLAARKATGIRKGISPMNRPPLSDKNIERYFPVLKRKA
          WGI.QNSGF.KN.L..R...MPGKRRPYGV.TGLAARKA..I.KG.SP.NR.PL.DKN.E.YFPVLKRKA
Retrocopy WGI*QNSGFDKNSLSCR--VMPGKRRPYGVVTGLAARKAARIQKGMSPTNRLPLGDKNRE*YFPVLKRKA

Parental  NLLRQNEVQRKP-VAVLKRPNQLNRKSNIPANFTRSGNKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLD
          NLLRQNEVQRKP..AVLK.PNQ.N.K.NIP.NFTRSGNKLSHQKD..QATF.FRRGLKVQAQLNTEQLLD
Retrocopy NLLRQNEVQRKP<IAVLKKPNQ*NGKNNIPVNFTRSGNKLSHQKDIHQATFIFRRGLKVQAQLNTEQLLD

Parental  DVVAKRTRQWRTSTTNGGILTVSIDNPGA-VQCPVTQKPRLTRTSVPSFLAKR-EQSDI-KKVPKGVPLQ
          DVVAKRTRQW.TSTTNGGI.....DNPGA.VQ..VTQK..LT...VPSFL..R.EQSDI.K..PKGVPLQ
Retrocopy DVVAKRTRQWWTSTTNGGISSIHTDNPGA<VQSSVTQKLCLTQPVVPSFLTIR<EQSDI<KVIPKGVPLQ

Parental  FDINSVGK
          FDINSV.K
Retrocopy FDINSVEK

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	22.56 RPM
SRP012922_cerebellum	0.00 RPM	20.62 RPM
SRP012922_heart	0.00 RPM	13.69 RPM
SRP012922_kidney	0.00 RPM	13.96 RPM
SRP012922_liver	0.00 RPM	8.82 RPM
SRP012922_lung	0.00 RPM	35.28 RPM
SRP012922_quadricep_muscle	0.00 RPM	39.98 RPM
SRP012922_spleen	0.00 RPM	34.57 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_2013 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 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013 , retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,