RetrogeneDB ID: retro_mdom_1330

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:37486829..37487653(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSMODG00000006565
• Aliases: None
• Description: chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]

Sequence

>retro_mdom_1330
AAAACTGAGATGGCCAGAGATCAGGCAGTGCTGGCTGTGAACATGAGTGCTGTCCAGGGCATACAGGATGTGCTAAGGAC
TGACCTGGGGCCCAAGGGCACTATGAAGATGTTCTTATTGGTTGCCAGAGACATCAAGTTCACCTAGGATGGCAATGTAC
TGTTACATGAGATGCAAATTCAACATCCAAAAACCTCCTTAATAGCCAAAGTGGCTACAGCCGAGGATGACATTACTCAA
GATGGTACTATTTCAAATGTTCTCATTATTGGAGAGCTACAGGCTAATCTCTACATCTCTGAAGAGCTACACCCTCAGAT
AAGAATTGAAGGATTTGAAGCTGCCAAGACAAAAGGCGCTTGGAACAAGGGAAATCATGAAGGAAATAGATAGGGAAATT
CTCGAAGATGTTACGTGAGCATCTCTGCACACCAAAGTCAATGCTGACCTAGCTGACATGCTGACTGAGGCAGTAGTAGA
CTCTATTTTGACTGTCAGAGAATCTGGTGAACTTGATCTTTTCATGGTAGATATCATGGAGATGAAGCATAAATGAGAAA
CTGAAACATCATTGATTAGAGGACTGTTTTTTTGGATCAGGGTGCCTGACACCCTGATATAAAGAAAGAGTAGAAGATGC
TTATATCCTTACATGCAATGTGTCATCAGAATATGAAAAAAACAGAAGTGAATTCTGGATTTTTTTTACAAGAGTGAAGA
GGAGAGAGAAGCTAGTAAAAGCAGAAAGGAAATTCTTTGAAGATAGAGTAAAGCAAAAAGTAGAACTGAAAAGAAAAATA
TGCAGTCGTTCAGACAAAGGATTT

Alignment

ORF - retro_mdom_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.54 %
• Parental protein coverage: 51.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQIQHPTASLIAK
          K.E.AR.QA.LAVN.SA..G.QDVLRT.LGPKGTMKM....A.DIK.T.DGNVLLHEMQIQHP..SLIAK
Retrocopy KTEMARDQAVLAVNMSAVQGIQDVLRTDLGPKGTMKMFLLVARDIKFT*DGNVLLHEMQIQHPKTSLIAK

Parental  VATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKT-KALEVLEQVKISKEIDREIL
          VATA.DDIT.DGT.SNVLIIGEL..QA.LYISE.LHP.I..EGFEAAKT.KAL...E..K...EIDREIL
Retrocopy VATAEDDITQDGTISNVLIIGEL--QANLYISEELHPQIRIEGFEAAKT>KALGTREIMK---EIDREIL

Parental  IDVARTSLRTKVNADLADVLTEAVVDSILTVRKPGEPVDLFMVEIMEMKHKSETDTSLIRGL-VLDHGAR
          .DV...SL.TKVNADLAD.LTEAVVDSILTVR..GE..DLFMV.IMEMKHK.ET.TSLIRGL.....G..
Retrocopy EDVT*ASLHTKVNADLADMLTEAVVDSILTVRESGE-LDLFMVDIMEMKHK*ETETSLIRGL>FFGSGCL

Parental  HPDMKKRVEDAYILTCNVSLEYE-KTEVNSGFFYKS-AEEREKLVKAERKFIEDRVKKIVELKRKVCGDS
          .P..K.RVEDAYILTCNVS.EYE.KTEVNSG.........REKLVKAERKF.EDRVK..VELKRK.C..S
Retrocopy TP*YKERVEDAYILTCNVSSEYE>KTEVNSGXXXQE<VKRREKLVKAERKFFEDRVKQKVELKRKICSRS

Parental  DKGF
          DKGF
Retrocopy DKGF

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1330 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,