RetrogeneDB ID: retro_rnor_1936

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:158414606..158415024(-)
• Located in intron of: ENSRNOG00000006921

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tfam
• Ensembl ID: ENSRNOG00000000613
• Aliases: Tfam, Mttfa
• Description: Transcription factor A, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q91ZW1]

Sequence

>retro_rnor_1936
CTTTGCAGTCCAATGCTTTTCATTCAACTTGGGAAATTATCCAAGAAAACTATGAGAGGATACCTTCAGTTGTCTACAGA
ACAGCTACCCAGACTTAACACTAAACACCACCACATGTGAAGCTTTCAGAACTGGTAAAAACATTGTGTCCCTGTGGAGG
GAACTACCAGACTCAGAAGAAAAAGTTATAAGGCTAATTTTAAGGCGGAATAAAAAGCATACAAGGAAGCTGTGAGCGGT
TTTAAGAACAGTCGACTCCAAGTCAGCTGATGGCTTCTGAGAAAGAAATCAGGCAAAAATGCTTAAAAATGAGTTATTAA
AAAGAAGAGAACAAATTTTTCTTGGAAGACCAAAAAGACATCAACCCGCACATACATTATCTGAAAGCTTCCAAGAGGCT
AAAGATAAATCTGCACAG

Alignment

ORF - retro_rnor_1936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.36 %
• Parental protein coverage: 58.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ICIPKCFSSLGNYPKKPMSSYLRFSTEQLPKFKAK-H-PDAKVSELIR-KIAAMWRELPEAEKKV-YEAD
          .C.P..F..LG...KK.M..YL..STEQLP....K.H.P..K.SEL....I...WRELP..E.KV.Y.A.
Retrocopy LCSPMLFIQLGKLSKKTMRGYLQLSTEQLPRLNTKHH<PHVKLSELVK<NIVSLWRELPDSEEKV<YKAN

Parental  FKAEWKVYKEAVSKYK-EQLTPSQLMGLEKEARQ-KRLKKKAQIKRRELILLGKPKRPRSAYNIYVSESF
          FKAE.K.YKEAVS..K.EQ.TPSQLM..EKE.RQ.K.LK......R.....LG.PKR...A.....SESF
Retrocopy FKAE*KAYKEAVSGFK<EQSTPSQLMASEKEIRQ<KMLKNELLKRREQI-FLGRPKRHQPAHTL--SESF

Parental  QEAKDESAQ
          QEAKD.SAQ
Retrocopy QEAKDKSAQ

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	16.75 RPM
SRP017611_kidney	0.00 RPM	34.54 RPM
SRP017611_liver	0.00 RPM	20.84 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1936 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1936 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,