RetrogeneDB ID: retro_ptro_2225

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:14800787..14802207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSPTRG00000019206
• Aliases: None
• Description: None

Sequence

>retro_ptro_2225
AAAGATGGCAATGTGCTGCTTCACGAAATGCAAATTCAACACACAACAGCTTCCTTAATAGCAAAGGTAGCAACAGCCCA
GGATGATATAACTGGTGATAGTACAACTTCCAATGTCCTAATCATTGAAAAGCTACTGAAACAGGCGGATCTCTACATTT
CTGAAGGCCTTCATCTCAGAATAATTACTGAAGGATTTGAAGCTGCAAAGGAAAAGGCCCTTCAGTTTTTGGAAGAAGTC
AAAGTAAGGAAAGAGATGGACAGGGAAACACTTATAAATGTGGCCAGAACATCTCTTCATACTAAAGTTCATGCTGAACT
TGCAGATGCCTTAACAGAGGCTGTAGTGGACTCCATTTTGGCCATTAAAAGACAAGATGAACCTATTGATCTCTTCATGG
TTGTGATCATGGAGATGAAACATAAATCTGAAACTGATACAAGCTTAATCAGAGGGCTTGTTTTGGACCACGGAGCATGG
CATCCTGATATGAAGAAAAGGGTGAAGGATGTATACATTCTCAAGCGTAACATGTCATTAGAATATGAAGAAACATAAGT
GAATTCTGGCTTTTTTTACAAGACTGCAGAAATGAGAGAAAAACTCATAAAAGCTGAAAGAAAATTCATTGAAGATAAGA
GTTAAAAAATAGAACTGAAAAGGAAAGTCTGTGGTGATTCAGATAAAGGATTTGTTGCTATTAATCAAGAGGGAATTGAC
CCCCTTTCCTTAGCTGCTCTTGCAAAAGAACACATAGTCACTCTTCACAGAGCTAAAAGGAGAAATATCGAGGGACTGAC
TCTTGCTTCTGGTGAGGTAGCCCTGAATTCTTTTGAAAACCTAAATCCTGACTGCTTGGGACATGCAGGACTTGTATATA
AATATATATTGGGAGAAGAGAAGTTCACCTTTATTGAGAAATGTAACAATACTCGCCCTGTCACATTATTAAACAAAGGA
CCAAATAAGTACACACTCACTCAGCTCAAAAGATGCAGTAAGGGATGGCTTGAGGGCTGTCAAAAATCCTATTGATGAGG
GCTGTGTGTTTCCAGGTGCTGGTGCTGTGGAAGTAGCAATGGCAGAAGCCCTGATTAAATATAAGCCCAGTGTAAAGGGC
AGGGCACAGCTTGGAGTCCACGCATTTGCTGATGTGTTGCTCATTATTCCAAAGGTTCTTGATCAGAACTCTGGTTTTGA
CCTTCAGGAAACATTAGTTAAAATTCAAGCAGAATGTTCAGAATCAGGTCAGCTTGTGGGTGTGGACCTGGACACAGGTG
AGCCAATGGTAGCAGCAGAAGTAGGCATATGGGATAACTATTGCGTAAAGAAACAGCTTCTTCACTCCTGCACTGTGATT
GCCACCAACATTCTCTTGGTTGATGAGATCATGCAAGCTGGAATGTTTTCTCTGAAAGGT

Alignment

ORF - retro_ptro_2225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 89.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAK
          KDGNVLLHEMQIQH.TASLIAKVATAQDDITGD.TTSNVLII..LLKQADLYISEGLH.RIITEGFEAAK
Retrocopy KDGNVLLHEMQIQHTTASLIAKVATAQDDITGDSTTSNVLIIEKLLKQADLYISEGLHLRIITEGFEAAK

Parental  EKALQFLEEVKVSREMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMIEIMEMK
          EKALQFLEEVKV..EMDRETLI.VARTSL.TKVHAELAD.LTEAVVDSILAIK.QDEPIDLFM..IMEMK
Retrocopy EKALQFLEEVKVRKEMDRETLINVARTSLHTKVHAELADALTEAVVDSILAIKRQDEPIDLFMVVIMEMK

Parental  HKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFI
          HKSETDTSLIRGLVLDHGA.HPDMKKRV.D.YIL..N.SLEYE.T.VNSGFFYK.AE.REKL.KAERKFI
Retrocopy HKSETDTSLIRGLVLDHGAWHPDMKKRVKDVYILKRNMSLEYEET*VNSGFFYKTAEMREKLIKAERKFI

Parental  EDRVKKIIELKRKVCGDSDKGFVVINQKGIDPFSLDALSKEGIVALRRAKRRNMERLTLACGGVALNSFD
          ED...K.IELKRKVCGDSDKGFV.INQ.GIDP.SL.AL.KE.IV.L.RAKRRN.E.LTLA.G.VALNSF.
Retrocopy EDKS*K-IELKRKVCGDSDKGFVAINQEGIDPLSLAALAKEHIVTLHRAKRRNIEGLTLASGEVALNSFE

Parental  DLSPDCLGHAGLVYEYTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQI-KDAVRDGLRAVKNAIDDGC
          .L.PDCLGHAGLVY.Y.LGEEKFTFIEKCNN.R.VTLL.KGPNK.TLTQ..KDAVRDGLRAVKN.ID.GC
Retrocopy NLNPDCLGHAGLVYKYILGEEKFTFIEKCNNTRPVTLLNKGPNKYTLTQL>KDAVRDGLRAVKNPIDEGC

Parental  VVPGAGAVEVAMAEALIKHKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKIQAEHSESGQL
          V.PGAGAVEVAMAEALIK.KPSVKGRAQLGV.AFAD.LLIIPKVL.QNSGFDLQETLVKIQAE.SESGQL
Retrocopy VFPGAGAVEVAMAEALIKYKPSVKGRAQLGVHAFADVLLIIPKVLDQNSGFDLQETLVKIQAECSESGQL

Parental  VGVDLNTGEPMVAAEVGVWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG
          VGVDL.TGEPMVAAEVG.WDNYCVKKQLLHSCTVIATNILLVDEIM.AGM.SLKG
Retrocopy VGVDLDTGEPMVAAEVGIWDNYCVKKQLLHSCTVIATNILLVDEIMQAGMFSLKG

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_prefrontal_cortex	0.30 RPM	69.16 RPM
SRP007412_cerebellum	0.32 RPM	127.41 RPM
SRP007412_heart	0.06 RPM	70.04 RPM
SRP007412_kidney	0.05 RPM	108.24 RPM
SRP007412_liver	0.03 RPM	90.80 RPM
SRP007412_testis	0.32 RPM	88.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2225 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2225 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3290
Pongo abelii	retro_pabe_2719

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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,