RetrogeneDB ID: retro_rnor_1472

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:2503295..2503723(+)
• Located in intron of: ENSRNOG00000027089

Retrocopy information

• Ensembl ID: ENSRNOG00000049523
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Itgb3bp
• Ensembl ID: ENSRNOG00000009116
• Aliases: None
• Description: Centromere protein R [Source:UniProtKB/Swiss-Prot;Acc:Q5U1Z7]

Sequence

>retro_rnor_1472
GTTAAAAGATCACTGAAACTAGATGATCAGTTTGAAGACAATTCATTTGGTCCTTCAGAAATCATGAAGAAGAAAAGTAG
TACAGCTTATTCTCCAACTACTGGAACTTATCAGTTGAGCCATTTTCTTCTCCTACAACCCCCAGAGTACAAGAACACAG
AAACAGACCATCAAATGGAACAAGAAAACTGAATAACTTGAGCTCACCTGAAAGACAGGAGTCCACAGTGAAAGGCAGTG
ATGGACCAATGATGTTGCTATCTAAAATTGAGAGATCATCAGAGAAAACCATGGAGATAATGAACAATTTAAGTAGTGTA
CAGGTGTTGGAGGGCAACAGACAACTTGAAGATCTCATTGGTGTTTCCCTAGTACCATGCTCCTTAAAAAGAGAAGCGAG
AAAAACCAAAGAGCTAATGACAAAAGTA

Alignment

ORF - retro_rnor_1472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.03 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKRSLKLDDQFEENSFGPSKIMRKKSITAFSPTTGTYQLS-PFSSPRTPKEQEHRDGPSNGTRKWSVLSS
          VKRSLKLDDQFE.NSFGPS.IM.KKS.TA.SPTTGTYQLS.PFSSP.TP..QEHR..PSNGTRK...LSS
Retrocopy VKRSLKLDDQFEDNSFGPSEIMKKKSSTAYSPTTGTYQLS<PFSSPTTPRVQEHRNRPSNGTRKLNNLSS

Parental  PARQDSTVKGSDGFMMLLSKIERSSEKTMEIMKNLSSLQALEGNRQLEDLLGVSLVPCSLKSEAKKTKEL
          P.RQ.STVKGSDG.MMLLSKIERSSEKTMEIM.NLSS.Q.LEGNRQLEDL.GVSLVPCSLK.EA.KTKEL
Retrocopy PERQESTVKGSDGPMMLLSKIERSSEKTMEIMNNLSSVQVLEGNRQLEDLIGVSLVPCSLKREARKTKEL

Parental  MTKV
          MTKV
Retrocopy MTKV

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	3.09 RPM
SRP017611_kidney	0.00 RPM	3.07 RPM
SRP017611_liver	0.13 RPM	1.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1472 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030710	1 retrocopy	retro_btau_747,
Callithrix jacchus	ENSCJAG00000016555	3 retrocopies	retro_cjac_2618, retro_cjac_3850, retro_cjac_3991,
Mus musculus	ENSMUSG00000028549	1 retrocopy	retro_mmus_1547,
Rattus norvegicus	ENSRNOG00000009116	1 retrocopy	retro_rnor_1472 ,
Tursiops truncatus	ENSTTRG00000007480	1 retrocopy	retro_ttru_996,