RetrogeneDB ID: retro_cjac_2414

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:20191548..20192440(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSCJAG00000005496
• Aliases: None
• Description: None

Sequence

>retro_cjac_2414
GATGCTCAGCGAAGCTTGCCTGTGGGCCTGGAGGCCCGGCATAAACCCCGCAGAGCACGTCGTCACAGCGTACTAGGCTC
ACAGCTTTACATTCATCAGGGGTCTTTCCGTCCCAGAAATTCTCGCAGATCTGACAGGACCAAAAGGAGGTTGTGCTGAA
GGGTAAGGGAGGATCGATGCTCATGGTCGCCAAGAACTTTTATGGGGACAATGGCATCATGGGAGCGCAGGTGCCCCTGG
GCGCTGGGACTGCTCTAACCTGGAAGTATAATGGAAAAGATGAGGTCTGCCTGACCTTCTATAGTGATGGCGCTGCTAAT
CAGGGGCAGATATTCGAAACTTACAACATGGCAGCTTTCTGGAAATTACCTTGTGTTTTCATCTGTAAGAATAACCACTA
TGGAATGGGAACATCTGTTGAGAGAGCGGCAGCAGCACTGATTACCAGGAGAGAGGCGATTTCATTCCTGGGCTGACAGG
GGATGCAGTGGTATCCTGTGTGTCCCAGAGGCGACAAGGTTTGCCGCTGCCTGCCTGCTGTAGATCTGGGAAGGGGCCCA
TCCTGAAGGGGCTGCAGACTTAGCATTACCACGGACACAGCATGAGTGATCCTGGAGTCCGCTACCATACAGGAGAAGAC
ATTGAGGAAGTAAGAAGTAAGAGTGACCGTATTATGTTTCTCAAGGACATGATGGTGAACAGCAATCTTGCCAGTGTGGA
AGAATTAAAGGAAATTGATGTGGAAGTGAGGAGGGAAAGTGAGGATGCTGCCCAGTTCGCCACGGCCTATCCAGAGCCGC
CTTTGGAGGAGCTGGGCTACCACGTCTACTCCAGCGACCCACCTTTCTAAGTTCGTGGTGCCAATCAGTGGATCAAGTTT
AAGTCAGTCAGT

Alignment

ORF - retro_cjac_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.8 %
• Parental protein coverage: 68.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DGQEACCVGLEA-GINPTDHLITAYRAHGFTFTRGLSVREILAELTGRKGGCA-KGKGGSMHMYAKNFYG
          D.Q....VGLEA.GINP..H..TAY.AH.FTF.RGLSV.EILA.LTG.KGGCA.KGKGGSM.M.AKNFYG
Retrocopy DAQRSLPVGLEA>GINPAEHVVTAY*AHSFTFIRGLSVPEILADLTGPKGGCA>KGKGGSMLMVAKNFYG

Parental  GNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRYGMGTS
          .NGI.GAQVPLGAG.AL..KYNGKDEVCLT.Y.DGAANQGQIFE.YNMAA.WKLPC.FIC.NN.YGMGTS
Retrocopy DNGIMGAQVPLGAGTALTWKYNGKDEVCLTFYSDGAANQGQIFETYNMAAFWKLPCVFICKNNHYGMGTS

Parental  VERAAA-STDYYKRGDFIPGLRVDGM-DILCVREATRF-AA-AYCRSGKGPILMELQTYRYHGHSMSDPG
          VERAAA.STDY..RGDFIPGL..D....ILCV.EATRF.AA.A.CRSGKGPIL..LQT..YHGHSMSDPG
Retrocopy VERAAA<STDYQERGDFIPGLTGDAV<GILCVPEATRFAAA>ACCRSGKGPILKGLQT*HYHGHSMSDPG

Parental  VSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATADPEPPLEELGYHI
          V.Y.T.E.I.EVRSKSD.IM.LKD.MVNSNLASVEELKEIDVEVR.E.EDAAQFATA.PEPPLEELGYH.
Retrocopy VRYHTGEDIEEVRSKSDRIMFLKDMMVNSNLASVEELKEIDVEVRRESEDAAQFATAYPEPPLEELGYHV

Parental  YSSDPPFEVRGANQWIKFKSVS
          YSSDPPF.VRGANQWIKFKSVS
Retrocopy YSSDPPF*VRGANQWIKFKSVS

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	0.02 RPM	21.10 RPM
SRP051959_heart	0.02 RPM	90.09 RPM
SRP051959_kidney	0.00 RPM	43.55 RPM
SRP051959_liver	0.00 RPM	40.20 RPM
SRP051959_lung	0.02 RPM	18.79 RPM
SRP051959_lymph_node	0.00 RPM	14.70 RPM
SRP051959_skeletal_muscle	0.02 RPM	46.43 RPM
SRP051959_spleen	0.00 RPM	15.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2414 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016730	1 retrocopy	retro_amel_400,
Bos taurus	ENSBTAG00000019852	2 retrocopies	retro_btau_100, retro_btau_1807,
Callithrix jacchus	ENSCJAG00000005496	2 retrocopies	retro_cjac_2414 , retro_cjac_27,
Dipodomys ordii	ENSDORG00000011848	1 retrocopy	retro_dord_35,
Equus caballus	ENSECAG00000001964	1 retrocopy	retro_ecab_21,
Erinaceus europaeus	ENSEEUG00000005485	1 retrocopy	retro_eeur_580,
Homo sapiens	ENSG00000131828	1 retrocopy	retro_hsap_41,
Gorilla gorilla	ENSGGOG00000013574	1 retrocopy	retro_ggor_59,
Myotis lucifugus	ENSMLUG00000012932	2 retrocopies	retro_mluc_2363, retro_mluc_323,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Mustela putorius furo	ENSMPUG00000003269	1 retrocopy	retro_mputfur_812,
Mus musculus	ENSMUSG00000031299	2 retrocopies	retro_mmus_63, retro_mmus_631,
Nomascus leucogenys	ENSNLEG00000009805	1 retrocopy	retro_nleu_74,
Oryctolagus cuniculus	ENSOCUG00000014748	1 retrocopy	retro_ocun_264,
Pongo abelii	ENSPPYG00000020171	1 retrocopy	retro_pabe_129,
Pan troglodytes	ENSPTRG00000021717	1 retrocopy	retro_ptro_79,
Pteropus vampyrus	ENSPVAG00000005420	1 retrocopy	retro_pvam_1306,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,
Sus scrofa	ENSSSCG00000023643	2 retrocopies	retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus	ENSSTOG00000015433	1 retrocopy	retro_itri_1529,
Tupaia belangeri	ENSTBEG00000014313	1 retrocopy	retro_tbel_3327,
Tursiops truncatus	ENSTTRG00000000660	1 retrocopy	retro_ttru_1427,