RetrogeneDB ID: retro_dnov_1867

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_34314:679..1319(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSDNOG00000001221
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_dnov_1867
GCCAGCATTGATGAGAAGTGTGGGTTGTTCACAGGCTTAGTTCCAAGACTGTGTTCAGGAGCCCTTGGAACTGTGGTCCA
TGGTAAAGTTTTACAGCATTACGAGGAATGTGAAAAGGTTGAGGAATTAGGACCTGGGAATGTACAGAAAGAAGTGTCAT
CATCCTTTGACTGAGTTATCAAGGAGACAACTCGAGAGATGATGGCTCGTTCTGCTGCTACCCTCATCACACATCCCTTT
CATGTGATCACTTTAAGATCTAGGGTTCAATTCATTGGCAGAGAATCCAAATATTGTGGACTTTGTGAATCCATAGTAAC
CATCTATAGGGAAGAGGGCATCCTAGGATTTTTTTGCGGGTCTTATTCATCGCCTCCTAGGTGACATCATTTCTTTGTGG
CTCTGTAACTCACTGGCCTATCTCGTCAATACCTATGCACTGGACAGTGGGGTTTCTACCATGATTGAAATGAAGAGTTA
TTCCCAAGCTGTCACAGGATTTTTTGCCAGTATGTTGACCTATCCCTTTGTGCTTGTCTCTAATCTCATGTCTGTCAACA
ACTGTGGGCTTGCTGGTGGATCTCCTCCTTACTCCCCAATATATACTTCTTGGATAGATTGTTGGTGCATGCTACAAAGA

Alignment

ORF - retro_dnov_1867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 70.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASIDA-CGLFTDLVPRLCSGALGTVVHGKVLQHYQECEKVEELGTGNVQKEVSSSFDRVIKETTREMMAR
          ASID..CGLFT.LVPRLCSGALGTVVHGKVLQHY.ECEKVEELG.GNVQKEVSSSFD.VIKETTREMMAR
Retrocopy ASIDEKCGLFTGLVPRLCSGALGTVVHGKVLQHYEECEKVEELGPGNVQKEVSSSFD*VIKETTREMMAR

Parental  SAATLITHPFHVITLRSMVQFIGRESKYCGLCESIVTIYREEGILGFF-AGLIPRLLGDIISLWLCNSLA
          SAATLITHPFHVITLRS.VQFIGRESKYCGLCESIVTIYREEGILGFF.AGLI.RLLGDIISLWLCNSLA
Retrocopy SAATLITHPFHVITLRSRVQFIGRESKYCGLCESIVTIYREEGILGFF>AGLIHRLLGDIISLWLCNSLA

Parental  YLVNTYALDSGVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLMAVNNCGLAGGSPPYSPIYTSWIDCWC
          YLVNTYALDSGVSTM.EMKSYSQAVTGFFASMLTYPFVLVSNLM.VNNCGLAGGSPPYSPIYTSWIDCWC
Retrocopy YLVNTYALDSGVSTMIEMKSYSQAVTGFFASMLTYPFVLVSNLMSVNNCGLAGGSPPYSPIYTSWIDCWC

Parental  MLQK
          MLQ.
Retrocopy MLQR

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	7.20 RPM	162.38 RPM
SRP012922_cerebellum	2.47 RPM	55.26 RPM
SRP012922_heart	2.78 RPM	61.72 RPM
SRP012922_kidney	4.93 RPM	114.99 RPM
SRP012922_liver	4.95 RPM	123.23 RPM
SRP012922_lung	1.53 RPM	30.70 RPM
SRP012922_quadricep_muscle	4.33 RPM	75.29 RPM
SRP012922_spleen	1.95 RPM	35.25 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_1867 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867 ,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,