RetrogeneDB ID: retro_cjac_2702

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:22452175..22452933(+)
• Located in intron of: ENSCJAG00000015939

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF5
• Ensembl ID: ENSCJAG00000011001
• Aliases: None
• Description: polycomb group ring finger 5 [Source:HGNC Symbol;Acc:28264]

Sequence

>retro_cjac_2702
ATGGCTACCCAAAGCAAACACTTGGTGAAAGATTTTAATCCTTTCATTACCTGCTATATCTGTAAAGTGTATCTGATCAA
GCCAACAGCAGTGGTGGAATACTTCCTTACAGTCTCTAAGACTTGTATTGTTCAGCACTTTGACGATAGCAATGATTGCC
CAAGGTGTGGCAACCAAGTTCATGAGACAAAGCCATTAGAAATATTGAGATTGGACAATACGTTAGAGGAAATTATATTT
AAGCTGATCCCTGGATTACAAAACAAGGACTTGAGTTTGAATCTGAATTTCGGAAGAAAAATAAGCCTCAAGAAAATGGA
CAAGATGTTACTTCAAAAGTTGACAAACTGAAAGTGGATGACGAAGGTGATGAAAATCAAGATTATCATAGAAGTGACCC
ACAAATTGCTATCTGTCTAGATTGTTTATGAAATAATGGACTATCGGGGGACAGTGTAGTAAAGGGTTTAATGAAGAAAT
TCATTCGATGTTCTACACATGTAACTGTTGGAACTATTAAAACATTTCTAAGTTTAAAGCTAAAACTTCCAAGTTCTTAT
GAGTTGGATGTGCTGTGCAATGGTGAAATTATGGGGAAGGATCATACTATGGAATTCATCTACATGACAAGATGGCGACT
AAGAGGCGAAAACTTTCGGTGTTTGAACTGCTCAGGTTCGCAAGTCTGCTCTCAGGATGGCCCTTTGTATCAGTCATACC
TTATGGTATTGCAGTATCGACCAAGAATTGATTCTGGT

Alignment

ORF - retro_cjac_2702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQVHETNPLEMLR
          MATQ.KHLVKDFNP.ITCYICK.YLIKPT.V.E...T..KTCIVQHF.DSNDCPRCGNQVHET.PLE.LR
Retrocopy MATQSKHLVKDFNPFITCYICKVYLIKPTAVVEYFLTVSKTCIVQHFDDSNDCPRCGNQVHETKPLEILR

Parental  LDNTLEEIIFKLVPGLR-EQELERESEFWKKNKPQENGQDVTSKVDKPKVDEEGDENQDYHRSDPQIAIC
          LDNTLEEIIFKL.PGL...Q.LE.ESEF.KKNKPQENGQDVTSKVDK.KVD.EGDENQDYHRSDPQIAIC
Retrocopy LDNTLEEIIFKLIPGLQ<KQGLEFESEFRKKNKPQENGQDVTSKVDKLKVDDEGDENQDYHRSDPQIAIC

Parental  LDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFIYM
          LDCL.NNG.SGD.VVKGLMKKFIRCST.VTVGTIK.FLSLKLKLPSSYELDVLCNGEIMGKDHTMEFIYM
Retrocopy LDCL*NNGLSGDSVVKGLMKKFIRCSTHVTVGTIKTFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFIYM

Parental  TRWRLRGENFRCLNCSASQVCSQDGPLYQSYPMVLQYRPRIDFG
          TRWRLRGENFRCLNCS.SQVCSQDGPLYQSY.MVLQYRPRID.G
Retrocopy TRWRLRGENFRCLNCSGSQVCSQDGPLYQSYLMVLQYRPRIDSG

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	0.40 RPM	99.98 RPM
SRP051959_heart	2.40 RPM	111.21 RPM
SRP051959_kidney	0.98 RPM	92.38 RPM
SRP051959_liver	1.34 RPM	63.05 RPM
SRP051959_lung	0.83 RPM	91.68 RPM
SRP051959_lymph_node	0.91 RPM	95.34 RPM
SRP051959_skeletal_muscle	2.27 RPM	71.00 RPM
SRP051959_spleen	0.86 RPM	105.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2702 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2702 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Callithrix jacchus	ENSCJAG00000011001	1 retrocopy	retro_cjac_2702 ,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Equus caballus	ENSECAG00000016162	1 retrocopy	retro_ecab_213,
Microcebus murinus	ENSMICG00000012035	5 retrocopies	retro_mmur_1358, retro_mmur_1499, retro_mmur_253, retro_mmur_858, retro_mmur_982,
Procavia capensis	ENSPCAG00000007871	1 retrocopy	retro_pcap_302,