RetrogeneDB ID: retro_cjac_515

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:34246598..34247333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V0D2
• Ensembl ID: ENSCJAG00000000343
• Aliases: None
• Description: None

Sequence

>retro_cjac_515
TCTCACCTATATGACAGTGCGATTCTGCTGATGAATGGTGCATTGCAGACAAAATCTGTGAAAGAAATTCCAGGGAAGTG
CCACCCCTTGGGCCGTTTCACATAAATGGAAGCTGTCAACATTGCAGAGACACCTTCAGATCCCTTTAATGCCTTTCTGG
TCGAAACACCATTAGCTCCATTCTTTCAAGACTGCATGTCTGTAAATGCTCTAGATGAACTGAATATTTAATTGCTGTAC
AATAAACTGTATAAATCTTACCTTGAGACATTCTATAAATTCTGTAAGAATCATGGTGATGTCACAGCAGAAGTTATGTG
TCCCATTTTTGAGTATGAGGCCAACAGACATGCTTTTATCAATACTCTTAACTCCTTTGGCACTGAATTGAGCAAAGAAG
ACTGGGAGACCCTCTATCCATCCTTCAGCAAGCTCTATCCTGAGGGGTTGCGGCTGTTGGCTCAAGCAGAAGACTTTGAC
CAGATGAAGAGCATAGCAGATCATTACGGAGTACACAAGGCTTTATTTGAAGCTGTAGGTGGCAGTGGGGGAAAGACATT
GGAGGACGTGTTTTATGAGCATGAGGTACAAATGAATGTGCTGGCATTCAACAGACAGTTCCACTACAGTGTGTTTTATG
CATATATAAAGCTGAAGGAACAGGAAATGAGAAATATTGTGTGGATACATTCACAGAGGCATCAAATGAAAATCAACAGT
TACATTCCAATTTTA

Alignment

ORF - retro_cjac_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 70.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYMIDNVILLMNGALQKKSVKEILVKCHPLGRFTEMEAVNIAETPSDLFNAILVETPLAPFFQDCMSENA
          S...D..ILLMNGALQ.KSVKEI..KCHPLGRFT.MEAVNIAETPSD.FNA.LVETPLAPFFQDCMS.NA
Retrocopy SHLYDSAILLMNGALQTKSVKEIPGKCHPLGRFT*MEAVNIAETPSDPFNAFLVETPLAPFFQDCMSVNA

Parental  LDELNIELLRNKLYKSYLETFYKFCKNHGDVTAEVMCPILEFEADRRAFIITLNSFGTELSKEDRETLYP
          LDELNI.LL.NKLYKSYLETFYKFCKNHGDVTAEVMCPI.E.EA.R.AFI.TLNSFGTELSKED.ETLYP
Retrocopy LDELNI*LLYNKLYKSYLETFYKFCKNHGDVTAEVMCPIFEYEANRHAFINTLNSFGTELSKEDWETLYP

Parental  AFGKLYPEGLRLLAQAEDFDQMKTIADHYEVYKPLFEAVGGNGGKTLEDVFYEREVQMNVLAFNRQFHYG
          .F.KLYPEGLRLLAQAEDFDQMK.IADHY.V.K.LFEAVGG.GGKTLEDVFYE.EVQMNVLAFNRQFHY.
Retrocopy SFSKLYPEGLRLLAQAEDFDQMKSIADHYGVHKALFEAVGGSGGKTLEDVFYEHEVQMNVLAFNRQFHYS

Parental  VFYAYVKLKEQEMRNIVWIAECISQRHRTKINSYIPIL
          VFYAY.KLKEQEMRNIVWI....SQRH..KINSYIPIL
Retrocopy VFYAYIKLKEQEMRNIVWIH---SQRHQMKINSYIPIL

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	0.24 RPM
SRP051959_heart	0.00 RPM	0.02 RPM
SRP051959_kidney	0.00 RPM	18.46 RPM
SRP051959_liver	0.00 RPM	0.02 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.04 RPM	0.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_515 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_515 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008749	1 retrocopy	retro_cfam_477,
Callithrix jacchus	ENSCJAG00000000343	1 retrocopy	retro_cjac_515 ,