RetrogeneDB ID: retro_rnor_1480

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:14138847..14139970(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmc6
• Ensembl ID: ENSRNOG00000007203
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:RefSeq peptide;Acc:NP_001093979]

Sequence

>retro_rnor_1480
CGAAGGCTTCTCATCATGGCGGACCCTAGAGATAAGGCGCTTCAGGACTACCGGAAGAAGCTCCTAGAGCACAAGCAGTG
TGAAAAGTCTGAAAATGATCTGAAGGCACTCCAAAATGTTGGACAGATTGTAGGGGAAGTGCTTAAACAGTTAACAGAAG
AAAAATTCATTGTTAAAGCAACAAATGGACCAAGATACGTCGTAGGTTGCCGTCAGCAGCTTGATAAAAGTACGCTGAAA
CCAGGAACAAGAGTTACTTTGGATATGACCACCCTAACCATCATGAGGTATCTGCCGAGAGAGGTGGATCCATTGTTTTA
TAACATGTCTCATGAGGATCCTGGAAATGTATCTTATTCTGAGGTTGGAGGCCTGTCAGAACAGATTCAGGAATTAAGAG
AGGTAATAGAATTATCTCTTACAAATCCAGAATTATTCCAGCGTGTAGGAATAATACTTCCAAAAGGCTGTTTGCTATAT
GGACCACCAGGCACTGAGAAAACACTCTTGTCACGAGCTGTTGCCAGCCAGCTAGACTGCAACTTCGTAAAGGTTGTATC
TAGTTCTATTGTAGACTAGTACATTGGTGAAAGTGCTCATTTGATTAGAGAAATGCTTAATTATGCCAGGGACCACCAGT
CATGCATCATTTTTATGGATGAAATAGATGCTATTGGTCGGTTTTCTGAGGGAACATCATCAGACAAAGAGATTCATAGA
ACTTTAATGGGAGTTACTAAATGAAATGGATGGATTTGATACTCTGCATAGAGTTAAAATGATCATGGCTACAAACAGAC
CAGATACACTGGATCCTGCTTTGCTGCACCCAGGAAAATTAGATAGAAAAATACATATCAATTTACCAAATAAACAAGCA
AGATTAGATATATTGAAAATCCACACAGGCCCTATTACAAAACATGGTGAAATAGATTATGAAGCCATTGTAGAGCTTTC
AGATGGTTTTAATGGAGCAGACCTGAGAAATGTTTACACTGAAGCAGGTATGTTTGCAATTCGTGCCGATCATGATTTTG
TAGTTCAGGAAGACTTCATGAAAGGAGTCAGAAAAGTGGCTGACTCCAAGAAGCTAGAGTCCAAACTGGACTATGAACCT
GTG

Alignment

ORF - retro_rnor_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 93.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEEKFIVKATNGPRYVVG
          R..L......D..L...R..L.E..KQ.EKSENDLKALQ.VGQIVGEVLKQLTEEKFIVKATNGPRYVVG
Retrocopy RRLLIMADPRDKALQDYRKKLLE-HKQCEKSENDLKALQNVGQIVGEVLKQLTEEKFIVKATNGPRYVVG

Parental  CRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELP
          CR.QLDKS.LKPGTRV.LDMTTLTIMRYLPREVDPL.YNMSHEDPGNVSYSE.GGLSEQI.ELREVIEL.
Retrocopy CRQQLDKSTLKPGTRVTLDMTTLTIMRYLPREVDPLFYNMSHEDPGNVSYSEVGGLSEQIQELREVIELS

Parental  LTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYA
          LTNPELFQRVGII.PKGCLLYGPPGT.KTLL.RAVASQLDCNF.KVVSSSIVD.YIGESA.LIREM.NYA
Retrocopy LTNPELFQRVGIILPKGCLLYGPPGTEKTLLSRAVASQLDCNFVKVVSSSIVD*YIGESAHLIREMLNYA

Parental  RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM-ELLNQMDGFDTLHRVKMIMATNRPDTLDPALLR
          RDHQ.CIIFMDEIDAIG..RFSEGTS.D.EI.RTLM.ELLN.MDGFDTLHRVKMIMATNRPDTLDPALL.
Retrocopy RDHQSCIIFMDEIDAIG--RFSEGTSSDKEIHRTLM>ELLNEMDGFDTLHRVKMIMATNRPDTLDPALLH

Parental  PGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHDF
          PG.LDRKIHI.LPN.QARLDILKIH.GPITKHGEIDYEAIV.LSDGFNGADLRNV.TEAGMFAIRADHDF
Retrocopy PGKLDRKIHINLPNKQARLDILKIHTGPITKHGEIDYEAIVELSDGFNGADLRNVYTEAGMFAIRADHDF

Parental  VVQEDFMKAVRKVADSKKLESKLDYKPV
          VVQEDFMK.VRKVADSKKLESKLDY.PV
Retrocopy VVQEDFMKGVRKVADSKKLESKLDYEPV

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	56.65 RPM
SRP017611_kidney	0.00 RPM	52.06 RPM
SRP017611_liver	0.00 RPM	41.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1480 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1480 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480 ,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,