RetrogeneDB ID: retro_mmul_2582

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:55730497..55731314(-)
• Located in intron of: ENSMMUG00000016725

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSMMUG00000015272
• Aliases: None
• Description: None

Sequence

>retro_mmul_2582
ATGGTGGCGGTGAAAACCCTGAACGCCAAGACCAAGGTGGCCGGAGCGCAGGCGGCCCTGTTGGTCAACATCAGCGCCGC
GCGGGGTCTGCAGGACGTGCTAAGGACCAACCTGGCACCCAAGGGCACCGTGAAGATGCTCGTTTCTGGCGCTGGAGACA
TCGAACTTACTAAAGACGGCAATGTGCTGCTTCACGAAATGCAAGTTCAACATCCAACAGCTTCCTTAATAGCAAAGGTA
GCAACAGGCCAGGATGATCTAACTGGTGATGCTAGGACTTCCAATATGCGTAATCATTGGAGAGCTAATGAAACAGGCGG
ATCTCTACATTTCTGAAGGCCTTCATCCCTGAATAACCGCTGAAGGATTTGAAGCTGCAAAGGAAAAGGCCCTTCAGTTT
TTGGAAGAAGTCAAAGTAAGCAGAGAGATGGACAGGGAAGCACTTATAGATGTGGCCAGAACACCTCTTCGTACTAAAGT
TCATGCTGAACTTGTAGATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTGGCCATTAAAAAACAAGATGAACCTATTG
ATCTCTTCATGATTGAGATCATGGAGATGAAACATAAATCTGAAACTGATAAAAGCTTAATCAGAGGGCTTGTTTTGGAC
CACGGAGCATGGCATCCTGATATGAAGAAAAGGGTGGAGGATGCATACGTCCTCACCTGTAACGTATCATTAGAGTATGA
AAAAACAGAAGTGAATTCTGGCTCTTTTTTTTACAAAAGTGCAGAAGAGAGAGAAAAACTCCTAAAAGCTTAAAGAAAAT
TCATTGAAGATAGAGTT

Alignment

ORF - retro_mmul_2582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQIQ
          M.AVKTLN.K..VA.AQAAL.VNISAARGLQDVLRTNL.PKGT.KMLVSGAGDI.LTKDGNVLLHEMQ.Q
Retrocopy MVAVKTLNAKTKVAGAQAALLVNISAARGLQDVLRTNLAPKGTVKMLVSGAGDIELTKDGNVLLHEMQVQ

Parental  HPTASLIAKVATAQDDITGDGTTSNV-LIIGELLKQADLYISEGLHPRIITEGFEAAKEKALQFLEEVKV
          HPTASLIAKVAT.QDD.TGD..TSN...IIGEL.KQADLYISEGLHP.I..EGFEAAKEKALQFLEEVKV
Retrocopy HPTASLIAKVATGQDDLTGDARTSNM>VIIGELMKQADLYISEGLHP*ITAEGFEAAKEKALQFLEEVKV

Parental  SREMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMIEIMEMKHKSETDTSLIRG
          SREMDRE.LIDVART.LRTKVHAEL.DVLTEAVVDSILAIKKQDEPIDLFMIEIMEMKHKSETD.SLIRG
Retrocopy SREMDREALIDVARTPLRTKVHAELVDVLTEAVVDSILAIKKQDEPIDLFMIEIMEMKHKSETDKSLIRG

Parental  LVLDHGARHPDMKKRVEDAYVLTCNVSLEYEKTEVSSG-FFYKSAEEREKLVKAERKFIEDKV
          LVLDHGA.HPDMKKRVEDAYVLTCNVSLEYEKTEV.SG....KSAEEREKL.KA.RKFIED.V
Retrocopy LVLDHGAWHPDMKKRVEDAYVLTCNVSLEYEKTEVNSGXXXXKSAEEREKLLKA*RKFIEDRV

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	61.52 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	67.51 RPM
SRP007412_cerebellum	0.00 RPM	59.47 RPM
SRP007412_heart	0.00 RPM	50.17 RPM
SRP007412_kidney	0.00 RPM	70.19 RPM
SRP007412_liver	0.04 RPM	41.96 RPM
SRP007412_testis	0.08 RPM	48.02 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2582 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2582 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582 ,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,