RetrogeneDB ID: retro_cjac_3200

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:27318979..27319745(+)
• Located in intron of: ENSCJAG00000013333

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF75D
• Ensembl ID: ENSCJAG00000014531
• Aliases: None
• Description: None

Sequence

>retro_cjac_3200
ATGATGACAGAGCTGAAGGCAGATGTATACTTGAATCCCCAGATGGGGGCTATGTGGGAGACTAACACGTCTGTGAAAGA
AACTCCAGTCCCAGTAAGAAATACAGCACGTAAATAGGGTATGTTGGCCTGAGAGTGCTCACAGGCACTTCCAGAGCTTC
TGTTATCATGAAGCAGCTGGACCACTTGAGGCTACCAGCCAACTTCAGAAAGTATGCCATTAGCGATTGAGGCCAGAGAT
CCACTCAAAAAAGCAGATCTTGGAAATATTGATGTTAGAGTAGTTCCTGACCATTCTGCCCAAGGAGACCCAGAACTTGG
TGCAGAAGCATCATCCACAGAATATCAAACAGGCTCTGGTCCTGGTGAAATGCTTGAGAGAGAACCTGGTGGAACAAAGA
ATGAGGTCACAGCCCATGAGCTGGGAAAGGAGTCAGTGCTCTTGGGAGGAAAGCAGTGGCCCCAGGCTTCAAGTGGAAAC
CAGCAGAGCCCCAACCAAAGGATATGTTCCAGAAAGAATATTGGAATATATACAGGATGCTACAAGAATAGCTGAGCTGG
AATACTAATGACTAAATCCAGCCTGTATATGAACGAGCTGTGCATGCTCAATAAATTTTAGCCCATTCTGAGCAGAAAAG
CACCAAAGACTGGAAGATGACATCTGAGCTCATCCTGCCTGAGTCCCAGAGTTTGCTGACATTTGAGATGTGGCTGTGTA
TTTTTCTAAGGAAGAATGGCAATTATTGCATCCTCCTGAGAAGACT

Alignment

ORF - retro_cjac_3200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.05 %
• Parental protein coverage: 50.39 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MMRELKADACSSRQMRAIWDTSGSVKENP-SQSTKYSTQIESLG-PESACRHFWSFRYHEATGPLETISQ
          MM.ELKAD.....QM.A.W.T..SVKE.P.S.S.KYST.I...G.PESA.RHF.SF.YHEA.GPLE..SQ
Retrocopy MMTELKADVYLNPQMGAMWETNTSVKETP<SPSKKYST*IGYVG<PESAHRHFQSFCYHEAAGPLEATSQ

Parental  LQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV-EFFQRKPDGTKNEV
          LQK.CH..LRPEIHSK.QILE.L.LE.FL.ILPKETQN.VQKHHPQN.KQALVLV.E...R.P.GTKNEV
Retrocopy LQKVCH*RLRPEIHSKKQILEILMLE*FLTILPKETQNLVQKHHPQNIKQALVLV<EMLEREPGGTKNEV

Parental  TVHELGKEAVLLGGT-AVAPGFKWKPAEPQPTGVFQKEYWNTYWVLQEQLGWNTHKETQPVYERAVHDQQ
          T.HELGKE.VLLGG..AVAPGFKWKPAEPQP...FQKEYWN.Y..LQE.L.WNT....QPVYERAVH.Q.
Retrocopy TAHELGKESVLLGGK<AVAPGFKWKPAEPQPKDMFQKEYWNIYRMLQE*LSWNTND*IQPVYERAVHAQ*

Parental  MLALSEQKSTKDWKMASEFILPASQSLLTFE-DVAVYFSEEEWQLLDPPEKT
          .LA.SEQKSTKDWKM.SE.ILP.SQSLLTFE.DVAVYFS.EEWQLL.PPEKT
Retrocopy ILAHSEQKSTKDWKMTSELILPESQSLLTFE<DVAVYFSKEEWQLLHPPEKT

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	0.98 RPM	0.51 RPM
SRP051959_heart	1.07 RPM	0.54 RPM
SRP051959_kidney	0.82 RPM	0.89 RPM
SRP051959_liver	0.32 RPM	0.56 RPM
SRP051959_lung	0.26 RPM	1.09 RPM
SRP051959_lymph_node	0.11 RPM	2.92 RPM
SRP051959_skeletal_muscle	1.27 RPM	0.22 RPM
SRP051959_spleen	0.40 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3200 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3200 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1108
Pongo abelii	retro_pabe_918

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014531	2 retrocopies	retro_cjac_3200 , retro_cjac_917,
Homo sapiens	ENSG00000186376	1 retrocopy	retro_hsap_797,
Otolemur garnettii	ENSOGAG00000032383	1 retrocopy	retro_ogar_1516,
Pongo abelii	ENSPPYG00000020747	1 retrocopy	retro_pabe_918,