RetrogeneDB ID: retro_dnov_461

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5008:37896..38461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSDNOG00000016631
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_dnov_461
TTCCTTTCCCCACTATCGCTGGCACCGAGATCCTTTAGTTTGCAGCTACCTCTACTACAGAAACGTGGACTAACCCTTAT
AATGTGCCCAACACAAAATACTGAAGCAGACTTTATTAAACCAAGCTTTCAGCAATTAATTAGTTATTTAGTCTTGGATA
TTGCAGATAATCCAGTTGAAAATATAATACATGTTTTCCCCCCATGACTACAGAATTTGTTGATAGGAGCTTATAAACTG
GAGGAAACATTCATGTCCGTGGAAATGCAGGGCTTTCCAGGAGTGTGGCTTTGGTTATTGCATACATTATGGGAATATTT
GTAATGAGCTACAAAGATGCATTTGCTTATATTGAAGAAAGAAGATTTTGTTTTAATCCTAATGCTGGATTCGTCATCAA
CTTCAGGATTTTGAAGCCATCTACCTAGCAAAATTTACAATACAGATAATGTCATCACTGTAGATAAAATGATCAATTTC
TGTCCATTCTGGTACCACAGGCAGTTTGAAGAGAACACGTGAAGAAGATGGTTTTTGAAATATGCGAGTGGCCATTGCAC
AGAAT

Alignment

ORF - retro_dnov_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 83.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLGPYSSAMKS---KLPILQKHGITHIICIRQNIEANFIKPNFQQLFRYLVLDIADNPVENIIRFFPM-T
          FL.P.S.A..S....LP.LQK.G.T.I.C..QN.EA.FIKP.FQQL..YLVLDIADNPVENII..FP...
Retrocopy FLSPLSLAPRSFSLQLPLLQKRGLTLIMCPTQNTEADFIKPSFQQLISYLVLDIADNPVENIIHVFPP*L

Parental  KEFIDGSFQ-TGGKVLVHGNAGISRSAAFVIAYIMETFGMKYRDAFAYVQERRFCINPNAGFV-HQLQEY
          .....G....TGG...V.GNAG.SRS.A.VIAYIM..F.M.Y.DAFAY..ERRFC.NPNAGFV.HQLQ..
Retrocopy QNLLIGAYK<TGGNIHVRGNAGLSRSVALVIAYIMGIFVMSYKDAFAYIEERRFCFNPNAGFV<HQLQDF

Parental  EAIYLAKLTIQMMSPVQIERSLSVHSGTTGSLKRTHEEDDDFGNMQVATAQN
          EAIYLAK.TIQ.MS...I..S.SVHSGTTGSLKRT.EE.D.F.NM.VA.AQN
Retrocopy EAIYLAKFTIQIMSSL*IK*SISVHSGTTGSLKRTREE-DGF*NMRVAIAQN

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	0.19 RPM	6.03 RPM
SRP012922_cerebellum	0.00 RPM	3.44 RPM
SRP012922_heart	0.00 RPM	4.64 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	2.63 RPM
SRP012922_lung	0.00 RPM	4.89 RPM
SRP012922_quadricep_muscle	0.00 RPM	11.77 RPM
SRP012922_spleen	0.00 RPM	5.61 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_461 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461 , retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,