RetrogeneDB ID: retro_cjac_1320

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:12375297..12376141(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSCJAG00000021279
• Aliases: None
• Description: None

Sequence

>retro_cjac_1320
GCATTCTTAATATCAAAAGTAGCAACAGCTCAAGATTATATAACCGGGGATGGTATGACTAACAATATCCTAATAACTAG
AGAGCTATTGAAGTAGGTGTACCTCTACATTTCTGAAGGCCTTCATCCCAGGATAATTACTGAAGGATTTGAGGCTGCAA
GGGTAAGGGCCTTTCCGTTCTTGGAACAAGTCAAAGTAAGCAGAGGGATAAACATAGAAACACTTAGACATGTGGCCAGA
ACATCTCTTAGTACTAAAGTTCATGCTGAACTTGCAGATGTCTTAACATAGGCTGTAATGGACTCCATTTTAACCATTAA
AAGACAAATGGAACCTGTTGATCTCTTCATATTTGAGATCATGGAGATGAAACATAAACCTGAAACTGATACAAGGTTAA
TTAGAGGGCTTGTTTTGGACCATGGAATATGGTGTCCTGATTTGAAGAAAATGGTGGAAGATGCATACATCCTCAAGTGT
CATGTGTCATTAGAATATGAAAAAAGGAAGCGAAATCTGGCTTTTTTATTTACAAGACCAAAGAAGAGAGAGAATACAAT
TACAAAATCGGAAAGAAAGTTCATTGAACATAGAGTTAAAAAATAATAAAACTAAAAAGGAAAGTCTGTGGTGAATCAGA
TAAAGGATTTGTTATTATCAAAAGTGAATTGAACTCTTTTCCTTAGATGTTCTTGCAAAAGAAGGCATACTAGCTCTACA
CAGAGCTGAAAGTAGAAATACAGAGAGTCTGACTCTTGATTATGGTGGGGTAGCTCTGATTTCTTTTGATGACCTAAATC
CTGACTGCTTAGGACATGCAGATCTTGTGTATGAGTATACATTG

Alignment

ORF - retro_cjac_1320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 56.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYVSEGLHPRIITEGFEAAKEKALQFLEEVKVSKEM
          A.LI.KVATAQD.ITGDG.T.N.LI..ELLK...LY.SEGLHPRIITEGFEAA...A..FLE.VKVS...
Retrocopy AFLISKVATAQDYITGDGMTNNILITRELLK*VYLYISEGLHPRIITEGFEAARVRAFPFLEQVKVSRGI

Parental  DRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPVDLFMIEIMEMKHKSETDTSLIRGLVLD
          ..ETL..VARTSL.TKVHAELADVLT.AV.DSIL.IK.Q.EPVDLF..EIMEMKHK.ETDT.LIRGLVLD
Retrocopy NIETLRHVARTSLSTKVHAELADVLT*AVMDSILTIKRQMEPVDLFIFEIMEMKHKPETDTRLIRGLVLD

Parental  HGARHPEMKKRVEDAYILTCNVSLEYE-KTEVNSGFF-YKSAEERE-KLVKAERKFIEDRIK-KIIELKR
          HG...P..KK.VEDAYIL.C.VSLEYE.K.E..SGFF.YK..EERE....K.ERKFIE.R.K.KII.LKR
Retrocopy HGIWCPDLKKMVEDAYILKCHVSLEYE<KKEAKSGFFIYKTKEERE>TITKSERKFIEHRVK<KIIKLKR

Parental  KVCGDSDKGFVVINQKGIDPF-SLDALSKEGIVALRRAKRRNMERLTLACGGVALNSFDDLSPDCLGHAG
          KVCG.SDKGFV.I.......F.SLD.L.KEGI.AL.RA..RN.E.LTL..GGVAL.SFDDL.PDCLGHA.
Retrocopy KVCGESDKGFVIIKSE-LNSF<SLDVLAKEGILALHRAESRNTESLTLDYGGVALISFDDLNPDCLGHAD

Parental  LVYEYTL
          LVYEYTL
Retrocopy LVYEYTL

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
SRP051959_colon	0.00 RPM	60.17 RPM
SRP051959_heart	0.00 RPM	76.44 RPM
SRP051959_kidney	0.00 RPM	69.35 RPM
SRP051959_liver	0.00 RPM	119.96 RPM
SRP051959_lung	0.00 RPM	67.40 RPM
SRP051959_lymph_node	0.00 RPM	92.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	125.50 RPM
SRP051959_spleen	0.00 RPM	80.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1320 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1320 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2741
Pan troglodytes	retro_ptro_1854

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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,