RetrogeneDB ID: retro_cjac_2037

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:5486940..5487874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSCJAG00000015550
• Aliases: None
• Description: None

Sequence

>retro_cjac_2037
ATTCGGAAATGTTTGACTTCTAATGTAGCATGTGGATCACCAACATTTGGGATATACAACTTGAACTGAAAGATTTCATA
CTTTTTGGCAGAAGAGGGAACTTGAACTTTATTAGGTTTCCAATCCGGTACCTGCCTACTTTTATCCAAATGGGAAGAGA
TAAAATCTTCTCAACATTGAAGACGATGCTTTGTGCTATAGGAGGTGGGGCTTACGAGTTTGAAAAAGATTTTGGCACAA
TTGGAAACCCCCAGCTGCACAAATTGGATGAACCTGACTGCCTTGTAAAGGGCTTGCTGTATACACTCTGTCAGTTTCAC
TGGACAGGTGGACTGCTATTATCTTGCTAATGCCTCAGACCCTGAGCGATGCCAAAAGCTGCGTTTTAACCTGGGTGATC
CCTATCCACTGCTTGTAGTGAACATTGGCTCAGGAGTCAGTATTCTAGCAGTCCATTCCAAAGACAACTATAAATGAGTG
ACTGAGACAAGCCTTTGGGGGGGGTGCCACTGTGGGTGTATGAAGTTTATTGACTGTCTGTGAAAGTTTTGAAGCCTTGA
GATGGCATCCAAAGGTGACAGCACACAAGCTGACAAGCTGGTCGGTGATATTTATGAAGGAGATGATGAAAGATTTGCTT
TGCCAGGTGGGGCTGTAGCATCTAGTTTTAGGATTATGATTTATAAGGAGAAGCAAGAATCTGTTGGTAAAGAAAATCTG
ACGAGCTACCTTAGTTACTATCACCACTAACACTGGTTCTGTGGCACGAAAGTGTGCTGTGAATGAATGAGTTGTCTTTG
TTGGAAACTTCCTACTTGTCAATACCTTCTCAATGAAAGTTTTGGCATATGCACTACATTGTCGGTCAAAAGGTCAACTG
AAAGCACTGTTTCTAGAACATGAGGGATACTGTGGAACAGTTGGTGTGCTTCTG

Alignment

ORF - retro_cjac_2037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.61 %
• Parental protein coverage: 85.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IRKYLTSNVAYGS-TGIRDVHLELKDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGG
          IRK.LTSNVA.GS.T.I.D..LELKD..LFGRRGNL.FIRFP...LPTFIQMGRDK.FSTL.T.LCA.GG
Retrocopy IRKCLTSNVACGS<TNIWDIQLELKDFILFGRRGNLNFIRFPIRYLPTFIQMGRDKIFSTLKTMLCAIGG

Parental  GAYKFEKDFRTIGNLHLHKLDELDCLV-KGLLY-IDSVSFNGQAECYYFANASEPERCQKMPFNLDDPYP
          GAY.FEKDF.TIGN..LHKLDE.DCLV.KGL...I.SVSF.GQ..CYY.ANAS.PERCQK..FNL.DPYP
Retrocopy GAYEFEKDFGTIGNPQLHKLDEPDCLV<KGLAV<IHSVSFTGQVDCYYLANASDPERCQKLRFNLGDPYP

Parental  LLVVNIGSGVSILAVHSKDNYKRVTGTSL-GGGTFLGLCSLLTGCESFEEAL-EMASKGDSTQADKLVRD
          LLVVNIGSGVSILAVHSKDNYK.VT.TSL.GGG...G..SLLT.CESF.EAL.EMASKGDSTQADKLV.D
Retrocopy LLVVNIGSGVSILAVHSKDNYK*VTETSL>GGGATVGV*SLLTVCESF-EAL<EMASKGDSTQADKLVGD

Parental  IYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLA-RATLVTITNNIGSVARMCAVNEKINRVVFVG
          IY.GD.ERF.LPG.AVASSF..MIYKEK.ESV.KE.L.........TN..GSVAR.CAVNE.....VFVG
Retrocopy IYEGDDERFALPGGAVASSFRIMIYKEKQESVGKENLT>ATLVTITTNT-GSVARKCAVNE*V---VFVG

Parental  NFLRVNTLSMKLLAYALDYWSKGQLKALFLEHEGYFGAVGALL
          NFL.VNT.SMK.LAYAL...SKGQLKALFLEHEGY.G.VG.LL
Retrocopy NFLLVNTFSMKVLAYALHCRSKGQLKALFLEHEGYCGTVGVLL

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	80.78 RPM
SRP051959_heart	0.00 RPM	41.62 RPM
SRP051959_kidney	0.00 RPM	71.04 RPM
SRP051959_liver	0.00 RPM	91.67 RPM
SRP051959_lung	0.00 RPM	54.17 RPM
SRP051959_lymph_node	0.00 RPM	49.84 RPM
SRP051959_skeletal_muscle	0.00 RPM	27.28 RPM
SRP051959_spleen	0.00 RPM	57.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2037 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037 ,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430, retro_nleu_144, retro_nleu_2975, retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994,