RetrogeneDB ID: retro_cjac_2345

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:64712524..64713229(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS4
• Ensembl ID: ENSCJAG00000005067
• Aliases: None
• Description: None

Sequence

>retro_cjac_2345
TCAGTGAAAGCTTTTGTGGAAGCAATGATAAATGAGAATGTTAGTCTCGTGATCTCAGGGCCGTTGTTGACTGATTTTTG
CACACATCTCCCTAACTTGCCTGATGGCACAGCCAAATAAATCTATCACTTCACCTTGGAAAAGATCCAGCCTAGAGTCA
TTTCATTTGAGGAGCAGTTTTCTTCCATAAGGCAGCATCTTGCATCCATATATGAGAAAGAAGATTGGAGAAATGCTGCC
CAAGTGTTGGTGGGAATTCCTTTGGAAACAGGACAAAAGCAATACAATGTAGATTATAAATGGGAGACTTACTTGAAGCT
TGCTAGGCTATGTCGGGAGGATGATGTTCCAGTCCAGGTGGAGGCTTACATAAATTGTGCATCATTGCTTCAGAATGAAT
CAGTCAATGAACAATTACTAATACATTATAAGGTATGCTATGCATGTGTTCTTGATTATAGAAGAAAATTCATTGAAGCT
GCACAAAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTTAAAGACAAGAGGCCATAAAACATGGTTAGCA
CTGTACCATCTTAGCATCAGCAGGACAGCAGTATTCTCAGATGCTAGTTACTCTTGAGGATGAAAAGTGCCAGCAACCTG
CTGCTTATGGGATTCTAGAGAAAATGTACCTAGATAGGATCATCAGAGGAAATCAGCTTCATAAA

Alignment

ORF - retro_cjac_2345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.65 %
• Parental protein coverage: 67.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALKAFVEAMVNENVSLVISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASI
          ..KAFVEAM.NENVSLVIS..LLTDFCTHLPNLPD.TAK.IYHFTLEKIQPRVISFEEQ..SIRQHLASI
Retrocopy SVKAFVEAMINENVSLVISGPLLTDFCTHLPNLPDGTAK*IYHFTLEKIQPRVISFEEQFSSIRQHLASI

Parental  YEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQL
          YEK.EDWRNAAQVLVGIPLETGQKQYNVDYK.ETYLK.ARL..EDD.PVQ.EAYIN.ASLLQNES.NEQL
Retrocopy YEK-EDWRNAAQVLVGIPLETGQKQYNVDYKWETYLKLARLCREDDVPVQVEAYINCASLLQNESVNEQL

Parental  QIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDE
          .IHYKVCYA.VLDYRRKFIEAAQRYNELSYKTIVHES.R.EA.KH..HCTILASAGQQ.S.ML.TL..DE
Retrocopy LIHYKVCYACVLDYRRKFIEAAQRYNELSYKTIVHES*RQEAIKHG*HCTILASAGQQYSQMLVTL-EDE

Parental  RCQQLAAYGILEKMYLDRIIRGNQLQE
          .CQQ.AAYGILEKMYLDRIIRGNQL..
Retrocopy KCQQPAAYGILEKMYLDRIIRGNQLHK

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	13.51 RPM
SRP051959_heart	0.00 RPM	15.52 RPM
SRP051959_kidney	0.00 RPM	15.86 RPM
SRP051959_liver	0.00 RPM	11.81 RPM
SRP051959_lung	0.00 RPM	12.17 RPM
SRP051959_lymph_node	0.00 RPM	14.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.12 RPM
SRP051959_spleen	0.00 RPM	14.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2345 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2345 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005067	2 retrocopies	retro_cjac_2148, retro_cjac_2345 ,
Monodelphis domestica	ENSMODG00000019311	1 retrocopy	retro_mdom_824,
Tupaia belangeri	ENSTBEG00000017599	2 retrocopies	retro_tbel_2134, retro_tbel_53,