RetrogeneDB ID: retro_mmul_348

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:35577184..35578297(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032481
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.1320
• Ensembl ID: ENSMMUG00000017768
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:RefSeq peptide;Acc:NP_001252763]

Sequence

>retro_mmul_348
ATGTCGCATCTGTCCCCCCAAGTCAAGCCCTCCAACCCCAGTAACCCTCGAGTCTTCTTTGACGTGGACATAGGAGGGGA
GCGAGTTGGTCGAATTGTCTTAGAATTCTTTGCAGATATTGTACCCAAAACTGCGGAAAATTTTCGTGCACTGTGTACAG
GAGAAAAAGGCATTGGACCCACGACTGGGAAACCTCTCCATTTCAAAGGATGCCCTTTTCATCGAATTATTAAGAAATTT
ATGATTCAGGGTGGAGACTTCTCAAATCAGAATGGGACAGGTGGAGAAAGTATTTATGGTGAAAAATTTGAAGATGAAAA
TTTCCACTATAAGCATGATCGGGAGGGTTTACTGAGCATGGCAAACGCAGGCCGCAACACAAATGGTTCTCAGTTTTTTA
TCACAACAGTTCCAACTCCTCATTTGGATGGGAAACATGTGGTGTTTGGCCAAGTAATTAAAGGAATAGGAGTGACAAGG
ATATTGGAAAATGTGGAAGTGAAAGGTGAAAAACCTGCTAAATTGTGCATTATTGCAGAATGTGGAGAATTGAAGGAAGG
AGATGACTGGGGAATATTCCCAAAAGATGGCTCTGGCGACAGTCATCCAGATTTCCCTGAGGATGCAGATGTAGATTTAA
AAGACGTAGATAAAATTTTATTAATAACAGAAGACTTAAAAAATATTGGAAATACTTTTTTCAAATCCCAGAACTGGGAG
ATGGCCATTAAAAAATATGCAAAAGTTTTAAGATACGTGGACAGTTCAAAGGCTGTTATTGAGACAGCAGATAGAGCCAA
GCTGCAACCTATAGCTTTAAGCTGTGTACTGAATATTGGTGCTTGTAAACTGAAGATGTCAAATTGGCAGGGAGCAATTG
ACAGTTGTTTGGAGGCTCTTGAAATAGACCCATCAAATACCAAAGCATTGTACCGCAGAGCTCAAGGATGGCAAAGATTA
AAAGAATATGATCAAGCATTGGCTGATCTTAAGAAAGCACAGGAGATAGCACCAGAAGATAAAGCTATCCAGGCAGAACT
GCTGAAAGTCAAACAACAGATAAAGGCACAGAAAGATAAAGAGAAGGCAGTATATGCAAAAATGTTTGCTTAG

Alignment

ORF - retro_mmul_348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHPSPQVKPSNPSNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKG
          MSH.SPQVKPSNPSNPRVFFDVDIGGERVGRIVLE.FADIVPKTAENFRALCTGEKGIGPTTGKPLHFKG
Retrocopy MSHLSPQVKPSNPSNPRVFFDVDIGGERVGRIVLEFFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKG

Parental  CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGRNTNGSQFFITTVPTP
          CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGRNTNGSQFFITTVPTP
Retrocopy CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGRNTNGSQFFITTVPTP

Parental  HLDGKHVVFGQVIKGIGVTRILENVEVKGEKPAKLCIIAECGELKEGDDWGIFPKDGSGDSHPDFPEDAD
          HLDGKHVVFGQVIKGIGVTRILENVEVKGEKPAKLCIIAECGELKEGDDWGIFPKDGSGDSHPDFPEDAD
Retrocopy HLDGKHVVFGQVIKGIGVTRILENVEVKGEKPAKLCIIAECGELKEGDDWGIFPKDGSGDSHPDFPEDAD

Parental  VDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIETADRAKLQPIALSCVLNIG
          VDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIETADRAKLQPIALSCVLNIG
Retrocopy VDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIETADRAKLQPIALSCVLNIG

Parental  ACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKV
          ACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQ.LKEYDQALADLKKAQEIAPEDKAIQAELLKV
Retrocopy ACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQRLKEYDQALADLKKAQEIAPEDKAIQAELLKV

Parental  KQKIKAQKDKEKAVYAKMFA
          KQ.IKAQKDKEKAVYAKMFA
Retrocopy KQQIKAQKDKEKAVYAKMFA

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
SRP007412_brain	0.11 RPM	5.38 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	13.33 RPM
SRP007412_cerebellum	0.00 RPM	6.01 RPM
SRP007412_heart	0.00 RPM	3.83 RPM
SRP007412_kidney	0.00 RPM	5.52 RPM
SRP007412_liver	0.04 RPM	2.69 RPM
SRP007412_testis	0.04 RPM	5.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_348 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Cavia porcellus	ENSCPOG00000001046	2 retrocopies	retro_cpor_275, retro_cpor_436,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348 ,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Mus musculus	ENSMUSG00000027804	6 retrocopies	retro_mmus_1086, retro_mmus_1888, retro_mmus_2228, retro_mmus_2555, retro_mmus_3254, retro_mmus_616,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,
Tursiops truncatus	ENSTTRG00000016269	1 retrocopy	retro_ttru_1027,