RetrogeneDB ID: retro_rnor_2652

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:124991374..124991921(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000009998
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vdac2
• Ensembl ID: ENSRNOG00000013505
• Aliases: None
• Description: Voltage-dependent anion-selective channel protein 2 [Source:UniProtKB/Swiss-Prot;Acc:P81155]

Sequence

>retro_rnor_2652
GCTGAGTGTTGTGTACCAGCATGTCCACGGCCAATGTGTATCCCTCCACCCTATGCTGACCTTGGCAAAGCTGCCAGAGA
CATTTTCAACAAAGGACTTGGCTTTGGGTTGGTAAAGTTGGTCGTGGAAACGACGTCATGCGGCGGTGTGGGGTTTTCAA
AATCTGACTCCTCTAATGCAGACACTGGCAAAGTCAGTGGGACCCTGGAGACCAAGTACAAACGGTGTGAGTATGGTCCG
ACTTTCATCAAGAAATGGAACACTGGACAACACTCTGGGGACAGGGATTGCAGTTGAAGACCTGATTTGTCAAGGTTTGA
AACTGACCTTGGACACCACGTCTTCACCGAACACAGGAAAGAAAAGTGTAAAAATCAAGTCTGCTTACAAGAGGGAATGT
ACAAACCTTGGCTATGATGTTGATTTTGATTTTGCTGGACCTGCCATCCATGGGTCAGCTGTCTTTGGTTACGAGGGCTG
GCTTGCTGGGTACCAATTGACTTTTGACAGTGCCAAGTCTAAGTCGACAAGGAGTAACTTCGCAGTT

Alignment

ORF - retro_rnor_2652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 61.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AECCVPVCQRPICIPPPYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVSGTLE
          AECCVP.C.RP.CIPPPYADLGKAARDIFNKG.GFGLVKL.V.T.SC.GV.FS.S.SSN.DTGKVSGTLE
Retrocopy AECCVPACPRPMCIPPPYADLGKAARDIFNKGLGFGLVKLVVETTSCGGVGFSKSDSSNADTGKVSGTLE

Parental  TKYKWCEYGLTFTEKWNT-DNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSAYKRECINLGCD
          TKYK.CEYG.TF..KWNT.DNTLGT.IA.ED.ICQGLKLT.DTT.SPNTGKKS.KIKSAYKREC.NLG.D
Retrocopy TKYKRCEYGPTFIKKWNT>DNTLGTGIAVEDLICQGLKLTLDTTSSPNTGKKSVKIKSAYKRECTNLGYD

Parental  VDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRSNFAV
          VDFDFAGPAIHGSAVFGYEGWLAGYQ.TFDSAKSK.TRSNFAV
Retrocopy VDFDFAGPAIHGSAVFGYEGWLAGYQLTFDSAKSKSTRSNFAV

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	146.52 RPM
SRP017611_kidney	0.84 RPM	191.90 RPM
SRP017611_liver	0.00 RPM	56.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2652 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Erinaceus europaeus	ENSEEUG00000008623	2 retrocopies	retro_eeur_192, retro_eeur_343,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Microcebus murinus	ENSMICG00000017815	1 retrocopy	retro_mmur_191,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Macaca mulatta	ENSMMUG00000008691	1 retrocopy	retro_mmul_2200,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Nomascus leucogenys	ENSNLEG00000016857	1 retrocopy	retro_nleu_1608,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000006375	8 retrocopies	retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652 ,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sorex araneus	ENSSARG00000011194	2 retrocopies	retro_sara_300, retro_sara_59,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Sus scrofa	ENSSSCG00000010320	2 retrocopies	retro_sscr_681, retro_sscr_791,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Tursiops truncatus	ENSTTRG00000000371	3 retrocopies	retro_ttru_116, retro_ttru_1172, retro_ttru_776,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,