RetrogeneDB ID: retro_pabe_2719

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:15491691..15493111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSPPYG00000025820
• Aliases: CCT6A, CCT6
• Description: T-complex protein 1 subunit zeta [Source:RefSeq peptide;Acc:NP_001125308]

Sequence

>retro_pabe_2719
AAAGATGGCAGTGTGCTGCTTCACGAAATGCAAATTCAACACACAACAGCTTCCTTAATAGCAAAGGTAGCAACAGCCCA
AGATGATATAACTGGTGATAGTACAACTTCCAATGTCCTAATCATTGAAAAGCTACTGAAACAGGCGGATCTGTACATTT
CTGAAGGCCTTCATCTCAGAATAATTACTGAAGGATTTGAAGCTGCAAAGGAAAAGGCCCATCGGTTTTTGGAAGAAGTC
AAAGTAAGGAAAGAGATGGACAGGGAAACACTTATAAATGTGGCCAGAACATCTCTTCATACTAAAATTCATGCTGAACT
TGCAAATACCTGAACAGAGGCTGTAGTGGACTCCATTTTGGCCATTAAAAGACAAGATGAACCTATTGATCTCTTCATGG
TTGTGATCATGGAGATGAAACATAAATATGAAACTGATACAAGCTTAATCAGAGGGCTTGTTTTGGACTACGGAGCATGG
CATCCTGATATGAAGAATAGGGTGGAGGATGTATACATTCTCAAGCGTAACGTGTCATCAGAATATGAAAAAACATAAGT
GAATTCTGGCTTTTTTTACAAGACTGCAGAAGAGAGAGAAAAACTCATAAAAGCTGAAAGAAAATTCATTGAAGATAAGA
GTTAAAAAATAGAACTGAAAAGGAAAGTCTGTGGTGATTCACATAAAAGATTTGTTGTTATTAATCAAGAGGGAATTGAC
CCCCTTTCCTTAGATGCTCTTGCAAAAGAACGCATAGTCACTCTTCACAGAGCTAAAAGAAGAAATACCGAGGGGCTGAC
TCTTGTTTGTGGTGAGGTAGCCCTGAATTCTTTTGACAACCTAAATCCTGACTGCTTGGGACATGCAGGACTTGTATATA
AATATACATTGGGAGAAGAGAAGTTCACCTTTATTGAGAAATGTAACAATACTCGCTCTGTCACATTATTGATCAAAGGA
CCAAATAAGCACACACTCACTCAGCTCAAAAGATGCAGTAAGGGATGGCTTGAGGGCTGTCAAAAATGCTATTGATGAGG
GCTGTGTGTTTCCAGGTGCTGGTGCTGTGGAGGTAGCAATGGCAGATGCCCTGATTAAATATAAGCCCAGTGTAAAGGGC
AGGGCACAGCTTGGAGTCCAAGCATTTGCTGATGTGTTGCTCATTATTCCAAAGGTTCTTGCTCAGAACTCTGGTTTTGA
CCTTCAGGAAACATTAGTTAAAATTCAAGCAGAATGTTCAGAATCAGGTCAGCTTGTGGGTGTGGACCTGGACACAGGTA
AGTCAATGGTAGTAGCAGAAGTAGGCATATGGGATAACTATTGTGTAAAGAAACAGCTTCTTCACTCCTGCACTGTGATT
GCCACCAACATTCTCTTGGTTGATGAGAACATGCAAGCTGGAATGTCTTCTCTGAAAGGT

Alignment

ORF - retro_pabe_2719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.68 %
• Parental protein coverage: 89.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAK
          KDG.VLLHEMQIQH.TASLIAKVATAQDDITGD.TTSNVLII..LLKQADLYISEGLH.RIITEGFEAAK
Retrocopy KDGSVLLHEMQIQHTTASLIAKVATAQDDITGDSTTSNVLIIEKLLKQADLYISEGLHLRIITEGFEAAK

Parental  EKALQFLEEVKVSREMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMIEIMEMK
          EKA..FLEEVKV..EMDRETLI.VARTSL.TK.HAELA...TEAVVDSILAIK.QDEPIDLFM..IMEMK
Retrocopy EKAHRFLEEVKVRKEMDRETLINVARTSLHTKIHAELANT*TEAVVDSILAIKRQDEPIDLFMVVIMEMK

Parental  HKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFI
          HK.ETDTSLIRGLVLD.GA.HPDMK.RVED.YIL..NVS.EYEKT.VNSGFFYK.AEEREKL.KAERKFI
Retrocopy HKYETDTSLIRGLVLDYGAWHPDMKNRVEDVYILKRNVSSEYEKT*VNSGFFYKTAEEREKLIKAERKFI

Parental  EDRVKKIIELKRKVCGDSDKGFVVINQKGIDPFSLDALSKEGIVALRRAKRRNMFRLTLACGGVALNSFD
          ED...K.IELKRKVCGDS.K.FVVINQ.GIDP.SLDAL.KE.IV.L.RAKRRN...LTL.CG.VALNSFD
Retrocopy EDKS*K-IELKRKVCGDSHKRFVVINQEGIDPLSLDALAKERIVTLHRAKRRNTEGLTLVCGEVALNSFD

Parental  DLSPDQLGHAGLVYEYTSGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQI-KDAVRDGLRAVKNAIDDGC
          .L.PD.LGHAGLVY.YT.GEEKFTFIEKCNN.RSVTLLIKGPNKHTLTQ..KDAVRDGLRAVKNAID.GC
Retrocopy NLNPDCLGHAGLVYKYTLGEEKFTFIEKCNNTRSVTLLIKGPNKHTLTQL>KDAVRDGLRAVKNAIDEGC

Parental  VVPGAGAVEVAMAEALIKHKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKIQAEHSESGQL
          V.PGAGAVEVAMA.ALIK.KPSVKGRAQLGVQAFAD.LLIIPKVLAQNSGFDLQETLVKIQAE.SESGQL
Retrocopy VFPGAGAVEVAMADALIKYKPSVKGRAQLGVQAFADVLLIIPKVLAQNSGFDLQETLVKIQAECSESGQL

Parental  VGVDLNTGEPMVAAEVGVWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG
          VGVDL.TG..MV.AEVG.WDNYCVKKQLLHSCTVIATNILLVDE.M.AGMSSLKG
Retrocopy VGVDLDTGKSMVVAEVGIWDNYCVKKQLLHSCTVIATNILLVDENMQAGMSSLKG

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	0.50 RPM	94.33 RPM
SRP007412_cerebellum	0.85 RPM	82.32 RPM
SRP007412_heart	0.18 RPM	55.90 RPM
SRP007412_kidney	0.43 RPM	127.65 RPM
SRP007412_liver	0.37 RPM	61.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2719 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2719 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2719 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3290
Pan troglodytes	retro_ptro_2225

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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,