RetrogeneDB ID: retro_rnor_453

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:80991243..80991568(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fkbp1a
• Ensembl ID: ENSRNOG00000008822
• Aliases: Fkbp1a, FKBP12, Fkbp2
• Description: Peptidyl-prolyl cis-trans isomerase FKBP1A [Source:UniProtKB/Swiss-Prot;Acc:Q62658]

Sequence

>retro_rnor_453
ATGGGAGTGCAGGTGGAGACCATCTCTCCTGGAGACCGGCGCACCTTCCCTAAGCGCCGCCAGACCTGCCTGGTACACTA
CACGGGAATGCTTGAAGATTGGAAGAAATTTGACTCCTCTCGGGACAGAAAAAAGCCTTTTAAGTTTACACTAGGCAAGC
AGGAGGTGATCCGAGGCTGGGAAGAAGGGGTAGCCCAGATAAGTGTGGGACAGAGAGCCAAACTGATAATCTCCCCCAGA
CTATTTCTGTGGAGCCACGGGGCACCCAGGCACCATCCCACCACATGCTACTCTTGTTTTTGATGTGGAGCTTCTAAAAC
TGGAA

Alignment

ORF - retro_rnor_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGVQVETISSGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFTLGKQEVIRGWEEGVAQMSVG
          MGVQVETIS.GD.RTFPKR.QTC.VHYTGMLED.KKFDSSRDR.KPFKFTLGKQEVIRGWEEGVAQ.SVG
Retrocopy MGVQVETISPGDRRTFPKRRQTCLVHYTGMLEDWKKFDSSRDRKKPFKFTLGKQEVIRGWEEGVAQISVG

Parental  QRAKLIIS-PDYAYGATGHPGIIPPHATLVFDVELLKLE
          QRAKLIIS.PDY..GATGHPG.IPPHATLVFDVELLKLE
Retrocopy QRAKLIIS>PDYFCGATGHPGTIPPHATLVFDVELLKLE

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	419.87 RPM
SRP017611_kidney	0.00 RPM	65.25 RPM
SRP017611_liver	0.00 RPM	63.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_453 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Dasypus novemcinctus	ENSDNOG00000005868	16 retrocopies	retro_dnov_1289, retro_dnov_1577, retro_dnov_1666, retro_dnov_2236, retro_dnov_228, retro_dnov_2404, retro_dnov_2418, retro_dnov_2544, retro_dnov_2589, retro_dnov_263, retro_dnov_584, retro_dnov_621, retro_dnov_670, retro_dnov_684, retro_dnov_707, retro_dnov_937,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mus musculus	ENSMUSG00000032966	1 retrocopy	retro_mmus_1293,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453 ,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,