RetrogeneDB ID: retro_rnor_1165

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:111944155..111944803(-)
• Located in intron of: ENSRNOG00000012751

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fkbp3
• Ensembl ID: ENSRNOG00000004629
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase FKBP3 [Source:RefSeq peptide;Acc:NP_001100206]

Sequence

>retro_rnor_1165
ATGGCGGCAGCTGTTCCTCAGCACACTTGGACTGTGGAGCAGCTGAGCAGTGAGCAGCTGCCCAAGGAGGACGTCATCAA
GTTTCTGCAGGATCACAGTTAAGACTCGTTTCTTGCAGAGCATAAATTACCGGGAAACAACACAACTAAAACTGCTAATA
AGGACCTTCTGGTTACTGCCTATCCCCATCTATTTGAAAGTAAGCGTTTCAAGGGTTCTGACTCTAAGTCAAGTATCTGG
ACAGGTGAAAAACGTGATATATGTGATAAACCAAAAGAACCCAAGTCTGAAGAGACTCTTGATGAGGATCCACCCAAATA
TACAAAATCTGTTCTAAGAAAGGGCGATAAAACCAACTTTCCTGAAAAGGGAGATGTTGTTCACAGCTGGCATACAGGGA
CACTCCCAGATGGAATTGTTTTTGATACTAATATTCAAACAAGTTCAAAGAAGAAGAAAAATGCCAAGCCTTTAAGCTTT
AAGGTTGGCGTGGGCCAGGGTATCAGAGGATGGGATGGGGCCTCTTGACTATGAGTAAAGGAGAAAGACCGGAGATTGAA
CCAGAATGCACCTATGGAAAGAAAGAAAGAACAGCCGGATGCCAAAATCCCACCAATCACCGAGCTCATTTCTGAAGTGG
AATTAGTG

Alignment

ORF - retro_rnor_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.3 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAVPQRAWTVEQLRSEQLPKKDIIKFLQDHGSDSFLAEHKLLGNIKNVAKTANKDHLVTAYNHLFESK
          MAAAVPQ..WTV........PK.D.IKFLQDH..DSFLAEHKL.GN..N..KTANKD.LVTAY.HLFESK
Retrocopy MAAAVPQHTWTVXXXXXXXXPKEDVIKFLQDHS*DSFLAEHKLPGN--NTTKTANKDLLVTAYPHLFESK

Parental  RFKGTETISKVSEQVKNVKLNDDKQKDSKSEETLDEGPPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTLP
          RFKG....S......K.......K....KSEETLDE.PPKYTKSVL.KGDKTNFP.KGDVVH.W.TGTLP
Retrocopy RFKGSDSKSSIWTGEKRDICDKPKE--PKSEETLDEDPPKYTKSVLRKGDKTNFPEKGDVVHSWHTGTLP

Parental  DGTVFDTNIQTSSKKKKNAKPLSFKVGVGKVIRGWDEA-LLTMSKGEKARLEIEPEWAYGKKGQ-PDAKI
          DG.VFDTNIQTSSKKKKNAKPLSFKVGVG..IRGWD.A.LLTMSKGE..R.EIEPE..YGKK........
Retrocopy DGIVFDTNIQTSSKKKKNAKPLSFKVGVGQGIRGWDGA<LLTMSKGE--RPEIEPECTYGKKERTAGCQN

Parental  PPNTKLIF-EVELV
          P.N....F.EVELV
Retrocopy PTNHRAHF>EVELV

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	0.14 RPM	66.86 RPM
SRP017611_kidney	0.07 RPM	34.75 RPM
SRP017611_liver	0.00 RPM	13.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1165 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165 ,
Rattus norvegicus	ENSRNOG00000008822	1 retrocopy	retro_rnor_453,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,