RetrogeneDB ID: retro_mmul_1084

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:112221347..112222829(+)
• Located in intron of: ENSMMUG00000023772

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10030
• Ensembl ID: ENSMMUG00000016118
• Aliases: None
• Description: dnaJ homolog subfamily C member 7 [Source:RefSeq peptide;Acc:NP_001248180]

Sequence

>retro_mmul_1084
ATGGCGGCTGCCGCGGAGTGCGACGTGGTAATGGCGGCGACCGAGCCAGAGCTGCTCGACGACGAAGAGGCGAAGAGGGA
AGCAGAGACTTTCAAGGAACAAGGAAATGCATACTATGCCAAGAAAGATTACAATGAAGCTTATAATTATTATACAAAAG
CCATAGATATGTGTCCTAAAAATGCTAGCTATTATGGTAATCGAGCAGCCACCTTGATGATGCTTGGAAGGTTCCGGGAA
GCTCTTGGAGATGCACAACAGTCAGTGAGGTTGGATGACAGTTTTGTCCGGGGACATCTACGAGAGGGCAAGTGCCATCT
CTCTCTAGGAAATGCCATGGCAGCATGTCGCAGCTTCCAGAGAGCCCTAGAACTGGATCATAAAAATGCTCAGGCACAAC
AAGAGTTCAAGAATGCTAATGCAGTCATGGAATATGAGAAAATAGCAGAAACAGATTTTGAGAAGCGAGATTTTCGGAAG
GTTGTTTTCTGCATGGACCGTGCCCTAGAATTTGCCCCTGCCTGCCATCGCTTCAAAATCCTCAAGGCAGAATGTTTAGC
AATGCTGGGTCGTTATCCAGAAGCACAGTCTGTGGCTAGTGACATTCTACGAATGGATTCTACCAATGCAGATGCTCTAT
ATGTACGAGGTCTTTGCCTTTATTATGAAGATTGTATTGAGAAGGCAGTTCAGTTTTTCGTATAGGCTCTCAGGATGGCT
CCTGACCATGAGAAAGCCTGCATTGCCTGCAGAAATGCCAAAGCACTCCAAGCAAAGAAAGAAGATGGGAATAAAGCATT
TAAGGAAGGAAATTACAAACTAGCATATGAACTGTACACAGAAGCCCTGGGGATAGACCCCAACAATATAAAAACAAATG
CTAAACTCTACTGTAATCGGGGTACGGTTAATTCCAAGCTTAGGAAACTAGATGATGCAATAGAAGACTGCACAAATGCA
GTGAAGCTTGATGACACTTACATAAAAGCCTACTTGAGAAGAGCTCAGTGTTACATGGACACAGAACAGTATGAAAAAGC
AGTACGAGACTATGAAAAAGTGTATCAGACGGAGAAAACAAAAGAACACAAACAGCTCCTAAAAAATGCACAGCTGGAAC
TGAAGAAGAGTAAGAGGAAAGATTACTACAAGATTCTGGGAGTGGACAAGAATGCCTCTGAGGACGAGATCAAGAAAGCT
TATCGGAAACGGGCCTTGATGCACCATCCAGATCGGCATAGTGGAGCCAGTGCTGAGGTTCAGAAGGAGGAGGAGAAGAA
GTTCAAGGAAGTTGGAGAAGCCTTTACTATCCTCTCTGATCCCAAGAAAAAGACTCGCTATGACAGTGGACAGGACCTAG
ATGAGGAGGGCATGAATATGGGTGATTTTGATCCAAACAATATCTTCAAGGCTTTCTTTGGCGGTCCTGGAGGCTTCAGC
TTTGAAGCATCTGGTCCAGGGAGTTTCTTTTTTCAATTTGGC

Alignment

ORF - retro_mmul_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAECDVVMAATEPELLDDEEAKREAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAA
          MAAAAECDVVMAATEPELLDDEEAKREAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAA
Retrocopy MAAAAECDVVMAATEPELLDDEEAKREAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAA

Parental  TLMMLGRFREALGDAQQSVRLDDSFVRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNAN
          TLMMLGRFREALGDAQQSVRLDDSFVRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNAN
Retrocopy TLMMLGRFREALGDAQQSVRLDDSFVRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNAN

Parental  AVMEYEKIAETDFEKRDFRKVVFCMDRALEFAPACHRFKILKAECLAMLGRYPEAQSVASDILRMDSTNA
          AVMEYEKIAETDFEKRDFRKVVFCMDRALEFAPACHRFKILKAECLAMLGRYPEAQSVASDILRMDSTNA
Retrocopy AVMEYEKIAETDFEKRDFRKVVFCMDRALEFAPACHRFKILKAECLAMLGRYPEAQSVASDILRMDSTNA

Parental  DALYVRGLCLYYEDCIEKAVQFFVQALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYT
          DALYVRGLCLYYEDCIEKAVQFFV.ALRMAPDHEKACIACRNAKAL.AKKEDGNKAFKEGNYKLAYELYT
Retrocopy DALYVRGLCLYYEDCIEKAVQFFV*ALRMAPDHEKACIACRNAKALQAKKEDGNKAFKEGNYKLAYELYT

Parental  EALGIDPNNIKTNAKLYCNRGTVNSKLRKLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEEAVRD
          EALGIDPNNIKTNAKLYCNRGTVNSKLRKLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYE.AVRD
Retrocopy EALGIDPNNIKTNAKLYCNRGTVNSKLRKLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEKAVRD

Parental  YEKVYQTEKTKEHKQLLKNAQLELKKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEV
          YEKVYQTEKTKEHKQLLKNAQLELKKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEV
Retrocopy YEKVYQTEKTKEHKQLLKNAQLELKKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEV

Parental  QKEEEKKFKEVGEAFTILSDPKKKTRYDSGQDLDEEGMNMGDFDPNNIFKAFFGGPGGFSFEASGPGSFF
          QKEEEKKFKEVGEAFTILSDPKKKTRYDSGQDLDEEGMNMGDFDPNNIFKAFFGGPGGFSFEASGPGSFF
Retrocopy QKEEEKKFKEVGEAFTILSDPKKKTRYDSGQDLDEEGMNMGDFDPNNIFKAFFGGPGGFSFEASGPGSFF

Parental  FQFG
          FQFG
Retrocopy FQFG

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	3.70 RPM	46.28 RPM
SRP007412_brain_prefrontal_cortex	2.62 RPM	57.67 RPM
SRP007412_cerebellum	3.23 RPM	35.26 RPM
SRP007412_heart	1.18 RPM	17.19 RPM
SRP007412_kidney	1.76 RPM	20.66 RPM
SRP007412_liver	0.48 RPM	4.95 RPM
SRP007412_testis	1.55 RPM	30.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1084 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1084 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084 , retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,