RetrogeneDB ID: retro_rnor_2373

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:69439685..69440380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Phb2
• Ensembl ID: ENSRNOG00000012999
• Aliases: Phb2, Bap, Bap-37, Bap37, Bcap27, Bcap37
• Description: Prohibitin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5XIH7]

Sequence

>retro_rnor_2373
TGGTTCCAGTACCCCATCATCTATAACATTCGGGCCAGACCTTGAAAAATCTCCACCCCTGCCCCCACAACAGGCTCCAA
AGACACGCAGATGGTGAACATCTCCCTGCTCATACTATCTCGGCCCAAGGCCCAGGAGCTCCCCAGAATGTACCAGTGCC
TAGGGCTAGACTACGAGGAGTGAGTGCTGCGGTCCATTGTAAATGGCCTGTGGCTCAAGAGTGTGGTGGCCAAGTTCAAT
ACCTCGCAGCTGATTACCAACGGGCTCAGGTGTCCCTGTTGATCCGAAGAGAGCTGACAGAACATGCCAAGGACTTCAGC
CTCATCCTGGATGATATAGCTATCACAGAGCTGAGCTTCAGCTGAGAGTACAAGCTGCTGTAGAAGCCGAACAAGTGGCC
CAGCAGGAAGTCCAGTGGGCCCAGTGTTGGGTGGAGAAAGCAAAGCAGGAACAATGACAGAAGATTGTGCAGCCTGAGGG
GGAGGCAGAGGCGGAGGCTGCCAAGATGCTTGGAGAAGCCCTGAGCAAGAATCCTGGCTATATCAAGCTCCCAAAGATCC
CGGCTGCCCAGAACGTCTCTAAGATGATCGCCACGTCACAGAACCGAATCCATCTCACAGCGGACAACCTTGTGCTGAAT
CTACAGGATGAACGCTTTACTGGGGGGAAGTGACAGCCTCATTAAGGGTAAGAAA

Alignment

ORF - retro_rnor_2373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.55 %
• Parental protein coverage: 75.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WFQYPIIYDIRARPRKISSP---TGSKDLQMVNISLRVLSRPNAQELPSMYQRLGLDYEERVLPSIVNEV
          WFQYPIIY.IRARP.KIS.P...TGSKD.QMVNISL..LSRP.AQELP.MYQ.LGLDYEE.VL.SIVN..
Retrocopy WFQYPIIYNIRARP*KISTPAPTTGSKDTQMVNISLLILSRPKAQELPRMYQCLGLDYEE*VLRSIVNGL

Parental  -LKSVVAKFNASQLIT-QRAQVSLLIRRELTERAKDFSLILDDVAITELSFSREYT-AAVEAKQVAQQEA
          .LKSVVAKFN.SQLIT.QRAQVSLLIRRELTE.AKDFSLILDD.AITELSFS.EY..AAVEA.QVAQQE.
Retrocopy WLKSVVAKFNTSQLIT<QRAQVSLLIRRELTEHAKDFSLILDDIAITELSFS*EYK<AAVEAEQVAQQEV

Parental  QRAQFLVEKAKQEQRQKIVQAEG--EAEAAKMLGEALSKNPGYIKLRKIRAAQNISKTIATSQNRIYLTA
          Q.AQ..VEKAKQEQ.QKIVQ.EG..EAEAAKMLGEALSKNPGYIKL.KI.AAQN.SK.IATSQNRI.LTA
Retrocopy QWAQCWVEKAKQEQ*QKIVQPEGEAEAEAAKMLGEALSKNPGYIKLPKIPAAQNVSKMIATSQNRIHLTA

Parental  DNLVLNLQDESFT-RGSDSLIKGKK
          DNLVLNLQDE.FT..GSDSLIKGKK
Retrocopy DNLVLNLQDERFT>GGSDSLIKGKK

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	47.02 RPM
SRP017611_kidney	0.00 RPM	129.17 RPM
SRP017611_liver	0.00 RPM	105.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2373 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373 ,