RetrogeneDB ID: retro_mmul_2094

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:91233819..91234482(-)
• Located in intron of: ENSMMUG00000001397

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13849
• Ensembl ID: ENSMMUG00000016512
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:F7G0S7]

Sequence

>retro_mmul_2094
ATGGCTGCGGCTGTTCCACAGCGGGCGTGGACCGTGGAGCAGCTGCGCAGTGAGCAGCTGCCCAAGAAGGACGTTATCAA
GTTTCTGCAGGAACACGGTTCAGATTCGTTTCTTGCAGAACATAAATTATTAGGAAACATTAAAAATGTGGCCAAGACAG
CTAACAAGGACCCCCTGGTTATAGCCTATAACCATCTTTTTGAAACTAAGCGTTTTAAGGGTACTGAAAGTATAAGTAAA
GTGTCTGAGCAAGTAAAAAATGTGAAGCTTAATGAAGATAAACCCAAAGAAACCAAGTCTGAAGAGACCCTGGATGAGGG
TCCACCAAAATATACTAAATCTGTTCTGAAAAAGGGAGATAAAACCAACTTTCCCAAAAAGGGAAAGTTGCTGGTATACA
GGAACACTACAAGATGGGACTGTTTTTGATACTAATATTCAAACAAGTGCAAAGAAGAAGAAAAATGCCAAGCCTTTAAG
TTTTAAGGTCGGAGTAGCAAAGTTATCAGAGGATGGGATGAAGCCCTCTTGACTATGAGTAAAGGAGAGAGGGCTCGACT
GGAGATTGAACCAGAATGGGCTTATGGAAAGAAAGCACAGCCTGATGCCAAAATTCCACCAAATTCAAAACTCATGTTTG
AAGTGGAATTAGTGGATATTGAC

Alignment

ORF - retro_mmul_2094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAVPQRAWTVEQLRSEQLPKKDIIKFLQEHGSDSFLAEHKLLGNIKNVAKTANKDHLVTAYNHLFETK
          MAAAVPQRAWTVEQLRSEQLPKKD.IKFLQEHGSDSFLAEHKLLGNIKNVAKTANKD.LV.AYNHLFETK
Retrocopy MAAAVPQRAWTVEQLRSEQLPKKDVIKFLQEHGSDSFLAEHKLLGNIKNVAKTANKDPLVIAYNHLFETK

Parental  RFKGTESISKVSEQVKNVKLNEDKPKETKSEETLDEGPPKYTKSVLKKGDKTNF-PKKGDVVHCWYTGTL
          RFKGTESISKVSEQVKNVKLNEDKPKETKSEETLDEGPPKYTKSVLKKGDKTNF.PK......CWYTGTL
Retrocopy RFKGTESISKVSEQVKNVKLNEDKPKETKSEETLDEGPPKYTKSVLKKGDKTNF>PKRES---CWYTGTL

Parental  QDGTVFDTNIQTSAKKKKNAKPLSFKVGVG-KVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKI
          QDGTVFDTNIQTSAKKKKNAKPLSFKVGV..KVIRGWDEALLTMSKGE.ARLEIEPEWAYGKK.QPDAKI
Retrocopy QDGTVFDTNIQTSAKKKKNAKPLSFKVGVA<KVIRGWDEALLTMSKGERARLEIEPEWAYGKKAQPDAKI

Parental  PPNAKLIFEVELVDID
          PPN.KL.FEVELVDID
Retrocopy PPNSKLMFEVELVDID

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	33.95 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.85 RPM
SRP007412_cerebellum	0.06 RPM	30.61 RPM
SRP007412_heart	0.12 RPM	42.93 RPM
SRP007412_kidney	0.00 RPM	15.49 RPM
SRP007412_liver	0.00 RPM	5.23 RPM
SRP007412_testis	0.15 RPM	20.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2094 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 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	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Macaca mulatta	ENSMMUG00000009587	1 retrocopy	retro_mmul_552,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
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,
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,