RetrogeneDB ID: retro_rnor_840

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:82644800..82645435(-)
• Located in intron of: ENSRNOG00000001925

Retrocopy information

• Ensembl ID: ENSRNOG00000022687
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Capg
• Ensembl ID: ENSRNOG00000013668
• Aliases: None
• Description: Macrophage-capping protein [Source:UniProtKB/Swiss-Prot;Acc:Q6AYC4]

Sequence

>retro_rnor_840
GGGGAGCAGTCCGACCTCTTCATGAGCTACTTCCCACCAGGCCTCAAGTACCGGGAAGGTGGTGTGGAGTCAACATTTCA
CAAGACAACCTCGCACGCCACGCCAGCAGTCGTCAGGAAGCTCTACCAGGTTAAGGGGAAGAAGAACATCCATGCGATTG
AGAGGGCTCTGAGCTGGGACAGCTTCAACACTGGGGACTGCCTCATCCTAGACCTGGCTCAGGACATCTTCGCCTGGTGT
GGAAAGTCCAGCATCTCTGGGGAGCAACATAGCGAGGGACCTGGCTTTGGCCATCCAGGACAGCGAGCGGCAGGGCAAGG
CCGAGGTAGAGATATCACTGATGAAGAAAAGCCAGCCAAGATGATCCAGGTTCTGTGTCCAAGCCTGCTCTAAAGGAAGG
CAACCCCGAGGAAGAAATTACAGCAGACCTGACTAACGCCCAGGCCGCAGCCCTGTGTAAGGTCTCTGATGCCACTGGGC
AGATGAATCTGACCAAGGTGGCTGACTCCCGCCCTTTTGCCTCTGAACTGCTAATTCCAGATGACTGCTTTGTTCTAGGC
AAGGATCTGTGTGGCAAAATCTACATTTGGAAGGGTGGAGCTTCTACCCCAGGACCAAGAAAGTCCCATCTTCAA

Alignment

ORF - retro_rnor_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 61.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GNESDLFMSYFPQGLKYREGGVESAFHKTTSGTTPAAIRKLYQVKGKKNIRATERALSWDSFNTGDCFIL
          G..SDLFMSYFP.GLKYREGGVES.FHKTTS..TPA..RKLYQVKGKKNI.A.ERALSWDSFNTGDC.IL
Retrocopy GEQSDLFMSYFPPGLKYREGGVESTFHKTTSHATPAVVRKLYQVKGKKNIHAIERALSWDSFNTGDCLIL

Parental  DLGQNIFAWCGGKSNI-LERNKARDLALAIRDSERQGKAQVEI-ITDGEEPAEMIQVLGP-KPALKEGNP
          DL.Q.IFAWC.GKS.I.L..N.ARDLALAI.DSERQGKA.VEI.ITD.E.PA.MIQVL.P.KPALKEGNP
Retrocopy DLAQDIFAWC-GKSSI>LGSNIARDLALAIQDSERQGKAEVEI<ITDEEKPAKMIQVLCP<KPALKEGNP

Parental  EEDITADQTNAQAAALYKVSDATGQMNLTKVADSSPFASELLIPDDCFVLDNGLCGKIYIWKGRKANEKE
          EE.ITAD.TNAQAAAL.KVSDATGQMNLTKVADS.PFASELLIPDDCFVL...LCGKIYIWKG.......
Retrocopy EEEITADLTNAQAAALCKVSDATGQMNLTKVADSRPFASELLIPDDCFVLGKDLCGKIYIWKGGASTPGP

Parental  RQAALQ
          R...LQ
Retrocopy RKSHLQ

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	2.08 RPM
SRP017611_kidney	0.00 RPM	15.35 RPM
SRP017611_liver	0.00 RPM	1.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_840 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_840 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019705	2 retrocopies	retro_cjac_3816, retro_cjac_459,
Macropus eugenii	ENSMEUG00000013559	1 retrocopy	retro_meug_1063,
Mus musculus	ENSMUSG00000056737	1 retrocopy	retro_mmus_3506,
Otolemur garnettii	ENSOGAG00000001084	1 retrocopy	retro_ogar_3277,
Rattus norvegicus	ENSRNOG00000013668	1 retrocopy	retro_rnor_840 ,
Rattus norvegicus	ENSRNOG00000015408	1 retrocopy	retro_rnor_2045,