RetrogeneDB ID: retro_mmul_2623

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:102069343..102070240(-)
• Located in intron of: ENSMMUG00000032385

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10037
• Ensembl ID: ENSMMUG00000010205
• Aliases: None
• Description: prohibitin-2 [Source:RefSeq peptide;Acc:NP_001253245]

Sequence

>retro_mmul_2623
ATGGCCCAGAACTTGAAGGACTTGGCAGGACGGCTGTCCGCCGGGCCCCGGGGCATGGGCACAGCACTGAAGCTGTTGCT
GGGGACCAGCGCCATGGCCTACAGTGTCCGTGAATCCGTGTTCACTGTGGAAGGTGGGCACAGAGCCATCTTCTTCAATT
GGATCAGTGGAGTGCAGCAGGACACTATCCTGGTCGAGGGCCTTCACTTCAGGATCCCCTGGTTCCAGTACCCCATTATC
TATGACATTCAGGCCAGATCTCGAAAAATCTCCTTCCCTATAGGCTCCAAAGACCTACAGATGGTGAATATCTCCCTGCA
AGTGCTGTCTCGACCCAATGCTCAGGAGCTTCCTAGCATGTACCAGCGCCTAGAGCTGAACTACGAGGAATGAGTGTTGC
CGTCCATTGCCAACGAGATGCTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCACAGCTGATCACCCAGCGGGCCCGGCTA
TCCCTGTTGATCCGCCGGGAGCTGACAGAGAGGGCCAAGGACTTCAGCCTTATCCTGGATGATGTGGCCATCACAGAGCT
GAGCTGTAGCAGAGAGTACACAGCTGCTGTAGAAGCCAAACAAGTGGCCCAGCAGGAGGCCCATCAGGCCCAATTCTTGG
TAGAAAAAGCGAAGCAGGAACAGCGGCAGAAAATTGTGCAGGCCGAGGGTGAGGCCGAGGCTGCCAAGATGCTTGGAGAA
GCACTGAGCAAGAACCCTGGCTACATCAAACTTCGTAAGATCCGAGCAGCCCAGAACATCTCCAAGACAATCGCCACATC
ACAGAATCATATTTATCTCACGGCTGACAACCTCGTGCTGAACCTACAGGATGAAAGTTTCACCAGAGGAAGTGATAGCC
TCATCAAGGGTAAGAAA

Alignment

ORF - retro_mmul_2623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQNLKDLAGRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRIGGVQQDTILAEGLHF
          MAQNLKDLAGRL.AGPRGMGTALKLLLG..A.AY.VRESVFTVEGGHRAIFFN.I.GVQQDTIL.EGLHF
Retrocopy MAQNLKDLAGRLSAGPRGMGTALKLLLGTSAMAYSVRESVFTVEGGHRAIFFNWISGVQQDTILVEGLHF

Parental  RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQELPSMYQRLGLDYEERVLPSIVNEV
          RIPWFQYPIIYDI.AR.RKIS.P.GSKDLQMVNISL.VLSRPNAQELPSMYQRL.L.YEE.VLPSI.NE.
Retrocopy RIPWFQYPIIYDIQARSRKISFPIGSKDLQMVNISLQVLSRPNAQELPSMYQRLELNYEE*VLPSIANEM

Parental  LKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQEAQRA
          LKSVVAKFNASQLITQRA..SLLIRRELTERAKDFSLILDDVAITELS.SREYTAAVEAKQVAQQEA..A
Retrocopy LKSVVAKFNASQLITQRARLSLLIRRELTERAKDFSLILDDVAITELSCSREYTAAVEAKQVAQQEAHQA

Parental  QFLVEKAKQEQRQKIVQAEGEAEAAKMISFCVRALSKNPGYIKLRKIRAAQNISKTIATSQNRIYLTADN
          QFLVEKAKQEQRQKIVQAEGEAEAAKM......ALSKNPGYIKLRKIRAAQNISKTIATSQN.IYLTADN
Retrocopy QFLVEKAKQEQRQKIVQAEGEAEAAKMLG---EALSKNPGYIKLRKIRAAQNISKTIATSQNHIYLTADN

Parental  LVLNLQDESFTRGSDSLIKGKK
          LVLNLQDESFTRGSDSLIKGKK
Retrocopy LVLNLQDESFTRGSDSLIKGKK

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	14.01 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	43.79 RPM
SRP007412_cerebellum	0.06 RPM	10.72 RPM
SRP007412_heart	0.18 RPM	30.03 RPM
SRP007412_kidney	0.70 RPM	34.74 RPM
SRP007412_liver	0.20 RPM	60.56 RPM
SRP007412_testis	0.11 RPM	17.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2623 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2623 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623 ,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,