RetrogeneDB ID: retro_dnov_1800

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_3108:106732..107459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSDNOG00000007258
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Sequence

>retro_dnov_1800
ATGCAATGTGCCAGCAAGCAAATCACCGCAAATAAGCTGTGCAAGGGCATCTAGACTGTGTGGTTTGTATCCCCAAGGAA
CAGGGAGTCCTTCCTTTTGGCACAGTAACCTGGCCAATGTCATCAGATACTTCCCCACCCAGGTACTCAACTTTGCCTTC
AAAGATAAATACAAGCAGAACTTCCTGGGTAGCGTGAACAAGAGGACCCGGGTCTGTTGCTACTTTGCAGGGAACCTGGC
ATCTGATGGGGCCACTGGAGACACATTCGTGTACCCTCTTGATTTTGCCAGTACCCATCTAGCCCCAGAAGTGGGGAAAG
CCACAGCAGAAAGGAAATTCAGAGGCCTTGGTGACTGCCTGATTAAGATGAACAAGTCCGATGGGATTAAGGGCCTGTAC
CGAGGCTATAATGTGTCAGTACAGGATATCTATCATAGATACTTCAGTATCTATGACACGGCAAAGGGAATGCTTCCTGA
TCCCAAGAATACCCACATCTTCATCAGCTGGATAATTGCACAGTCCGTGGCTGGGTTGACTTCCTATTCATTTGACACTG
TCCATAGCCTCATGATGATGCAGTCGGGGCCTCAAGGAACCGATTTCATGTACAAAGGCATGCTCAACTGGGAGCGGAAG
ATTGCTTGTGATGAAAGACCCAAAGCTTTTTTCAAGGGCACATGGCCCCATGTTCTCAGAGACATGAGTGGTGCTTTTGT
GCTTGTA

Alignment

ORF - retro_dnov_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VQHASKQITAEKQYKGI-IDCVVRIPKEQGFL-SFWRGTLANVIRYFPTQAINWAFKDKYKQIFLGGVDR
          .Q.ASKQITA.K..KGI..DCVV.IPKEQG.L.SFW...LANVIRYFPTQ..N.AFKDKYKQ.FLG.V..
Retrocopy MQCASKQITANKLCKGI<LDCVVCIPKEQGVL<SFWHSNLANVIRYFPTQVLNFAFKDKYKQNFLGSVNK

Parental  HKQFWRYFAGNLASGGAAGATSLCIVYPLDFARTRLAADVGKGAAQREFSGLGNCLTKIFKSDGLRGLYQ
          ......YFAGNLAS.GA.G.T....VYPLDFA.T.LA..VGK..A.R.F.GLG.CL.K..KSDG..GLY.
Retrocopy RTRVCCYFAGNLASDGATGDT---FVYPLDFASTHLAPEVGKATAERKFRGLGDCLIKMNKSDGIKGLYR

Parental  GFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQTVTAVAGLVSYPFDTVRRRMMMQSGRK
          G.NVSVQ..I..R..YF..YDTAKGMLPDPKN.HI..SW.IAQ....VAGL.SY.FDTV...MMMQSG..
Retrocopy GYNVSVQD-IYHR--YFSIYDTAKGMLPDPKNTHIFISWIIAQS---VAGLTSYSFDTVHSLMMMQSGPQ

Parental  GADIMYSGTVDCWRKIAKDEGAKAFFKGAWSNVLRGMGGAFVPV
          G.D.MY.G.....RKIA.DE..KAFFKG.W..VLR.M.GAFV.V
Retrocopy GTDFMYKGMLNWERKIACDERPKAFFKGTWPHVLRDMSGAFVLV

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	14.20 RPM
SRP012922_cerebellum	0.00 RPM	58.84 RPM
SRP012922_heart	0.00 RPM	2239.10 RPM
SRP012922_kidney	0.55 RPM	321.16 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.00 RPM	11.91 RPM
SRP012922_quadricep_muscle	0.00 RPM	2749.62 RPM
SRP012922_spleen	0.00 RPM	5.15 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_1800 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 14 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800 , retro_dnov_390,
Dasypus novemcinctus	ENSDNOG00000008384	1 retrocopy	retro_dnov_1894,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,