RetrogeneDB ID: retro_mmul_2599

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:77418855..77419759(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019708
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2599
ATGGCCCAGAACTTGAAGGACTTGCCGGGACGGCTGCCCGCAGGGCCCCGGGGCATGGGCACGGCATTGAAGCTGTTGCT
GGGGGCCGGCGCTGTGGCATACGGTGTCCGCGAATCCGTGTTCACTGTGGAAGGCGGGCATAGAGCCATCTTCTTCAATC
GGATCTGTGGAGTGCAGCAGGACACTATCCTGGCCGAGGGCCTTCACTTCAGGATCCCCTGGTTGCAGTACCCCATTATC
TACGACATTCGGGCCAGACCTCGAAAAATCTCCTCCCCTGCAGGCTCCAAAGACCTACAAATGGTGAATATCTCCCTGAG
AGTGCTGTCTCAACCCCAATGCTCAAGAGCTTCCTAGCATGTACCAGTGCCTAGGGCTGGACTACGAGGAACGAGTGCTG
CCGTCCATTGTCAACCAGGTGCTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCACAGCTGATCACCCAGCAGGCCCAGGT
ATCCCTGTTGATCCGCTGGGAGCTGACAGAGAGGGCCAAGGACTTCAGCCTCATCCTGGATGATGTAGCCATCACAGAGC
TGAGCTTTAGCCGAGAGTACACAGCTGCTGTAGAAGCCAAACAAGTGGCCCAGCAGGAGGTCCAGCGGGCCCAATTCTTG
GTAGAAAAAGCGAAGCAGGAACAGCGGCAGAAGACTGTGCAGGCCGAGGGTGAGGCCGAGGCTGCCAAGATGCTTGGAGA
AGCACTGAGCAAGAACCCTGGCTACATCAAACTTCACAAGATCCAAGCAGCCCAGAATATCTCCAAGACGATCGCCACAT
CATAGAACCGTATTTATCTCATGGCTGACAACCTCATGCTGAACCTACAGGATGAAAGTTTCACCAGAGGAAACTTTGGT
GACAGCCTCATCAAGGGTAAGAAA

Alignment

ORF - retro_mmul_2599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQNLKDLAGRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRIGGVQQDTILAEGLHF
          MAQNLKDL.GRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRI.GVQQDTILAEGLHF
Retrocopy MAQNLKDLPGRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRICGVQQDTILAEGLHF

Parental  RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRP-NAQELPSMYQRLGLDYEERVLPSIVNE
          RIPW.QYPIIYDIRARPRKISSP.GSKDLQMVNISLRVLS.P.NAQELPSMYQ.LGLDYEERVLPSIVN.
Retrocopy RIPWLQYPIIYDIRARPRKISSPAGSKDLQMVNISLRVLSQP>NAQELPSMYQCLGLDYEERVLPSIVNQ

Parental  VLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQEAQR
          VLKSVVAKFNASQLITQ.AQVSLLIR.ELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQE.QR
Retrocopy VLKSVVAKFNASQLITQQAQVSLLIRWELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQEVQR

Parental  AQFLVEKAKQEQRQKIVQAEGEAEAAKMISFCVRALSKNPGYIKLRKIRAAQNISKTIATSQNRIYLTAD
          AQFLVEKAKQEQRQK.VQAEGEAEAAKM......ALSKNPGYIKL.KI.AAQNISKTIATS.NRIYL.AD
Retrocopy AQFLVEKAKQEQRQKTVQAEGEAEAAKMLG---EALSKNPGYIKLHKIQAAQNISKTIATS*NRIYLMAD

Parental  NLVLNLQDESFTRGS--DSLIKGKK
          NL.LNLQDESFTRG...DSLIKGKK
Retrocopy NLMLNLQDESFTRGNFGDSLIKGKK

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	0.00 RPM	14.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	43.79 RPM
SRP007412_cerebellum	0.00 RPM	10.72 RPM
SRP007412_heart	0.00 RPM	30.03 RPM
SRP007412_kidney	0.00 RPM	34.74 RPM
SRP007412_liver	0.00 RPM	60.56 RPM
SRP007412_testis	0.00 RPM	17.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2599 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2599 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,