RetrogeneDB ID: retro_rnor_2289

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:52490099..52490984(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cfdp1
• Ensembl ID: ENSRNOG00000019326
• Aliases: None
• Description: Craniofacial development protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q75UQ2]

Sequence

>retro_rnor_2289
ATGGGAGAACTCGACTCTGAAGACTTCTCCACGTCGGATGAGGATGAGGACTACGTGTCATCGGGTGGCGAGTACAGTGA
AGATGATGTCAATGAATCGGTGAAGGAAGATGAAGTGGATGGTGAAGAGCGGGCTGAGAAAACCAAAGGGAAAAGAAGGA
AGGCTCAGAGCATTCCAGCCAGGAAGAGAAAACAAAGTGGCCTCTCGTTAGACGAAGAGGACGACGGCAGGGAAGACTCT
GGAGGTGGCAGTAGTGAAGAAGATGAAGAGGAGCAAGAAGGAGGCCTCGGGTCAGAGAATGCAAGGAAGAAGAAGGACGA
TGAACTGTGGGCCAGCCTCCTTAATGATGTAGGACCAAAGTCAAAAGCAGCCCCAAGTTCACAAGTCAAGGTAGCAGCGG
AGACTGAAGGGACTAGTTCAAGTGAACCATTGGTGAAAGCAGGTGAACTAGAGAAACCTAAAGAATCAGAAAAGGTGACG
ATTACCACGGTGTTTGACTTTGCTGGCAAAGAGGTAAGGGTGACTAAGGAAGTAGATGCCACATCTAAGGAAGCCAAGTC
TCTCCTCAAGCAAACAGAGAAAGAAAAACCACAGGCTCTTGTCACTTCAGCAGAGACACCACTCCCTGCTGGGTCAGGGA
TAAAAAGAACAAGTGGGATGAGCAGCCTTTTAGGAAAAATTGGAGCCAAGAAACAGAAAATGAGCACCCTTGAGAAATCC
AAATTGGACTGGGAGAGCTTCAAGGAAGAAGAAGGGATTGGTGAAGAGCTGGCCATCCATAACCGAGGGAAAGAAGGGTA
CATCGAACGGAAAGCTTTTCTGGAGCGCATGGACCACAGGCAGTTTGAAATTGAGCGAGATCTCAGGCTGAGCCAAATGA
AACCT

Alignment

ORF - retro_rnor_2289 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEFDSEDFSTSDEDEDYVPSGGEYSEDDVNELVKEDEVDGEEQAEKTKGKRRKAQSIPARKRKQSGLLL
          M.E.DSEDFSTSDEDEDYV.SGGEYSEDDVNE.VKEDEVDGEE.AEKTKGKRRKAQSIPARKRKQSGL.L
Retrocopy MGELDSEDFSTSDEDEDYVSSGGEYSEDDVNESVKEDEVDGEERAEKTKGKRRKAQSIPARKRKQSGLSL

Parental  DEEEDGEEDSGGSSREEDEEEQEGGLGSETSRKKKEDELWASFLNDVGTKSKAASSSQVKVAEETEETSS
          DEE.DG.EDSGG.S.EEDEEEQEGGLGSE..RKKK.DELWAS.LNDVG.KSKAA.SSQVKVA.ETE.TSS
Retrocopy DEEDDGREDSGGGSSEEDEEEQEGGLGSENARKKKDDELWASLLNDVGPKSKAAPSSQVKVAAETEGTSS

Parental  SKPLVKADELEKPKESEKVKITKVFDFAGEEVRVTKEVDATSKEAKSFLKQTEKEKPQALVTSAATPPPA
          S.PLVKA.ELEKPKESEKV.IT.VFDFAG.EVRVTKEVDATSKEAKS.LKQTEKEKPQALVTSA.TP.PA
Retrocopy SEPLVKAGELEKPKESEKVTITTVFDFAGKEVRVTKEVDATSKEAKSLLKQTEKEKPQALVTSAETPLPA

Parental  GSGIKRTSGMSSLLGKIGAKKQKMSTLEKSKLDWESFKEEEGIGEELAIHNRGKEGYIERKAFLERVDHR
          GSGIKRTSGMSSLLGKIGAKKQKMSTLEKSKLDWESFKEEEGIGEELAIHNRGKEGYIERKAFLER.DHR
Retrocopy GSGIKRTSGMSSLLGKIGAKKQKMSTLEKSKLDWESFKEEEGIGEELAIHNRGKEGYIERKAFLERMDHR

Parental  QFEIERDLRLSKMKP
          QFEIERDLRLS.MKP
Retrocopy QFEIERDLRLSQMKP

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	0.07 RPM	70.31 RPM
SRP017611_kidney	0.21 RPM	41.94 RPM
SRP017611_liver	0.00 RPM	20.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2289 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289 ,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,