RetrogeneDB ID: retro_ocun_1278

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:23742134..23742507(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSOCUG00000014405
• Aliases: None
• Description: transcription factor A, mitochondrial [Source:HGNC Symbol;Acc:11741]

Sequence

>retro_ocun_1278
AGTTTTGCGTATATTCCGAGATGGTGTTCATCCACCTTTGACAGCTATCCAAAGAAACCTATGATTTCATACCTTCAGTT
TTCTAAAGAACAGCTACCCATATTTAAAGCTCAGAACGGAGAGCTAATTAAAAAAAAAAATTGCCAAGCTGTGGAGGGAA
CTTCCTGATTTAGAGAAAAAGGTATATGAAGATGTTTATGGGGTAGAGTGGGAGGCCCACAAAGAGGAGATTAACCAAAT
TCAAGAAGCTCTAACTCCAAGTCAGATGCTATCTATGGAAATAGTAATCATGCAAAGACGTTTAAAAAAGAAAGCATTAA
TGAAAAAGTTAGCAATGCTTTGGAAATCAAAAAGATCCCACTGAGCTTATGAC

Alignment

ORF - retro_ocun_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 58.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFSYIPRWCSSTFGSYPKKPMTSYLRFS-KEQLPIFKAKNPEAKNSELIKRIAELWRELPDSEKKVYEDA
          SF.YIPRWCSSTF.SYPKKPM.SYL.FS.K...P..K........S.L.K.IA.LWRELPD.EKKVYED.
Retrocopy SFAYIPRWCSSTFDSYPKKPMISYLQFS>KNSYPYLKLRT----ES*LKKKIAKLWRELPDLEKKVYEDV

Parental  YRVEWEAYKEEISRIQEHLTPSQMLSMEKEIMQKRLKKKALMKKRELTMLGKPKRPRSAYN
          Y.VEWEA.KEEI..IQE.LTPSQMLSME..IMQ.RLKKKALMKK..L.ML.K.KR...AY.
Retrocopy YGVEWEAHKEEINQIQEALTPSQMLSMEIVIMQRRLKKKALMKK--LAMLWKSKRSH*AYD

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
SRP017611_brain	0.00 RPM	26.21 RPM
SRP017611_kidney	0.00 RPM	31.42 RPM
SRP017611_liver	0.00 RPM	13.57 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1278 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1278 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278 ,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,