RetrogeneDB ID: retro_cjac_43

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:50991301..50991805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023188
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002621
• Aliases: None
• Description: None

Sequence

>retro_cjac_43
GCAGGTGGGGAGACTCCTGGGGACACAGGTGGAGAGGGCACTGCTGCTGCGGGTCGGTTCAGATTCAGCCCAGAGCCCAC
GCTCAAGGACATCCGCCGCCTCCATGCTGAGTTTGCTGCTGAACGAGACTGGGAACAGTCCCATCAGCCTCGGAACCTCC
TCCTGGCCTTGGTTGGGGAAGTGGGGGAGCTGGCAGAACTCTTTCACTGGAAAACCAATGGGGAGCCTGGCCCCCAAGGC
TGGTCCTCCAGGGAACGGGCTGCCCTTCAAGAGGAGCTTAGTGATGTCCTCTTCTACCCGGTGGCATTAGCAGCCCGCTG
CCGTGTGGATCTGCCCCAAGCAGTGCTCTCCAAAATGGACATCAGCCGTCGACGCTACCCAGCCCATCTGGCCTGCAGCT
CTTCCCACAAGTATACAGAATTGCCCCACAGGACCATCTCTGAAGACCAGGCTGTGAAGCCCGCGGACTTTCCCTGTGAC
TCCATGGGCCAGGCCTCAACCTAG

Alignment

ORF - retro_cjac_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 98.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGGEAPGDTDGEGTAAAGRFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQW
          AGGE.PGDT.GEGTAAAGRF.FSPEPTL.DIRRLHAEFAAERDWEQ.HQPRNLLLALVGEVGELAELF.W
Retrocopy AGGETPGDTGGEGTAAAGRFRFSPEPTLKDIRRLHAEFAAERDWEQSHQPRNLLLALVGEVGELAELFHW

Parental  KTDGEPGPQGWSSRERAALQEELSDVLIYLVALAARCRVDLPQAVLSKMDINRRRYPAHLARSSSRKYTE
          KT.GEPGPQGWSSRERAALQEELSDVL.Y.VALAARCRVDLPQAVLSKMDI.RRRYPAHLA.SSS.KYTE
Retrocopy KTNGEPGPQGWSSRERAALQEELSDVLFYPVALAARCRVDLPQAVLSKMDISRRRYPAHLACSSSHKYTE

Parental  LPHGTISEDQAMGPSDLPCDSTGQAST
          LPH.TISEDQA..P.D.PCDS.GQAST
Retrocopy LPHRTISEDQAVKPADFPCDSMGQAST

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	2.20 RPM
SRP051959_heart	0.00 RPM	0.95 RPM
SRP051959_kidney	0.00 RPM	0.91 RPM
SRP051959_liver	0.00 RPM	1.26 RPM
SRP051959_lung	0.00 RPM	1.04 RPM
SRP051959_lymph_node	0.00 RPM	2.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.59 RPM
SRP051959_spleen	0.00 RPM	0.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_43 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_43 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016594	1 retrocopy	retro_cfam_887,
Callithrix jacchus	ENSCJAG00000002621	2 retrocopies	retro_cjac_43 , retro_cjac_676,
Myotis lucifugus	ENSMLUG00000013774	1 retrocopy	retro_mluc_1052,
Otolemur garnettii	ENSOGAG00000011361	1 retrocopy	retro_ogar_874,
Rattus norvegicus	ENSRNOG00000017850	2 retrocopies	retro_rnor_1173, retro_rnor_2626,
Sus scrofa	ENSSSCG00000007796	1 retrocopy	retro_sscr_676,