RetrogeneDB ID: retro_cjac_4051

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:35446172..35446630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD63
• Ensembl ID: ENSCJAG00000007935
• Aliases: None
• Description: CD63 molecule [Source:HGNC Symbol;Acc:1692]

Sequence

>retro_cjac_4051
CCAGAGGAAAGAGGCCCGGCAGCCATGGCAGTGGAAGGAGAAATGAAATGTGTGAAGTTCCTGCTTTCTGTCCTCCTGCT
GGCCTTTTGTGCCTGTGCAGTGGGACTGATTGCCGTGGTTGTCTGGCACAGCTTGTCTTCAGTCAGACCATAATCCAGGG
GGCTCCTCTGGCTTTCTGTTGCCTGTGGTCATCATCACAGTGGGTGTCTTCCTCTTCCTGGTGGCCTTTGTGGGCCACTG
TGGGCCCTGCAAGGAGAATTATTATCTTATGATCACGTTTGCCATCTTCCTGTCTCTTACCATGCTGGTAGATGTGGCTG
CAGCCATTGCTTGGCTGTGTGTTTAGAGATCAGATGATGTCAGAGTTTAATAACAACTTCTAGCAGCAGATGCAGAATTA
CCCAAAAAACAACCACGTGGCTCCAATCCTGGATAGGATGCAGGAAGATTTTAAGTGC

Alignment

ORF - retro_cjac_4051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 57.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSAPGPAAMAVEGGMKCVKFLLYVLLLAFCACAVGLIAV-GVGAQLVLSQTIIQGA-TPGSLLPVVIIAV
          P...GPAAMAVEG.MKCVKFLL.VLLLAFCACAVGLIAV.G..AQLV.SQTIIQGA...G.LLPVVII.V
Retrocopy PEERGPAAMAVEGEMKCVKFLLSVLLLAFCACAVGLIAV<GCLAQLVFSQTIIQGA<SSGFLLPVVIITV

Parental  GVFLFLVAFVGCCGACKENYCLMITFAIFLSLIMLVEVAAAIA-GYVFRDKVMSEFNNNFRQQMENYPKN
          GVFLFLVAFVG.CG.CKENY.LMITFAIFLSL.MLV.VAAAIA.G.VFRD..MSEFNNNF.QQM.NYPKN
Retrocopy GVFLFLVAFVGHCGPCKENYYLMITFAIFLSLTMLVDVAAAIA>GCVFRDQMMSEFNNNF*QQMQNYPKN

Parental  NHTASILDRMQTDFKC
          NH.A.ILDRMQ.DFKC
Retrocopy NHVAPILDRMQEDFKC

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	41.16 RPM
SRP051959_heart	0.00 RPM	64.44 RPM
SRP051959_kidney	0.00 RPM	69.82 RPM
SRP051959_liver	0.00 RPM	64.64 RPM
SRP051959_lung	0.00 RPM	49.81 RPM
SRP051959_lymph_node	0.00 RPM	27.17 RPM
SRP051959_skeletal_muscle	0.00 RPM	78.90 RPM
SRP051959_spleen	0.00 RPM	90.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4051 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4051 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4051 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011931	1 retrocopy	retro_btau_234,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Callithrix jacchus	ENSCJAG00000007935	1 retrocopy	retro_cjac_4051 ,
Cavia porcellus	ENSCPOG00000009142	1 retrocopy	retro_cpor_676,
Mus musculus	ENSMUSG00000025351	1 retrocopy	retro_mmus_1722,