RetrogeneDB ID: retro_cjac_2714

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:44141565..44142441(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC2
• Ensembl ID: ENSCJAG00000002149
• Aliases: None
• Description: None

Sequence

>retro_cjac_2714
ATGGGACATAAAGTGGTCATATTTGACATTTCTGTTGTCAGAGCCTTGTGGGAAACTCATGTCAAGAGCACAGTTTGGCA
GAAGAAGGAGGCAGAAAGTCTTGAGAAGAGTGCATTGGAAAAGACAAAGGAGGAGTGGAACCCTGAGGCCAAGTACAGGA
GGAAAGGCATCCCCCGGCACTGTATGCAAGAATAGCTTCAGAGACACCAACATGTGGCTTCTGGAAAAGATAGAAAGGAA
CGCTCTCATAAGGCAGAGATCACTTCCTAAGGACAGAGGCAAATGGAGCAGTGCATTTGTGTCTGGACTTTCTGGGGAGC
ACTGGACAGAGCTGCCAGATTTGTTGAAGATGCACCTGGGAGAACAGCATATATGCGACACTCTGATTCAAATCACTCCT
ACATATTATATTGAGCTGTTTCATTCGATGAGAATTCAGGATCTGCCAAAGACACAAATCTCACATCTTCCAGCTGAAAT
CAGTTGTTTGAAGAACCTGAAATAACTCAATGTGAGTTTCACCTATCTGAAAAGCATTTCTCCAGAACTGGGAGATGGTG
AAATCTAGAGAGACTGGATTGTTCTGGAAATCTAGAATTCATAGAGCTGCCTTTTGGGATTAAGTAATTGGAAACCAGTT
GCATTTGTAGATACCTATACAAACAAGTTTTTCACTGTCCCAATCTGTGTACTGAGGATGTCTATTTGCAGTGGTTGGAT
ATCAGCAATAACCTGACTGACCTGACACAAGATAGAGACAGGTTGGGAGAGCTGCAGGGCTTTCTCTTATACAAAATCAA
GTTGACCTACCTGCCTTATCATGAGCTTAACCTAAAGGAGCACACCTTATTAGTTGTCAATGGGGACCATTTGGTC

Alignment

ORF - retro_cjac_2714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGHKVVVFDISVLRALWETRVKKHKAWQKKEAERLEKSALEKIKEEWNFVAECRRKGIPQ-AVY-CKNGF
          MGHKVV.FDISV.RALWET.VK....WQKKEAE.LEKSALEK.KEEWN..A..RRKGIP..A.Y.CKN.F
Retrocopy MGHKVVIFDISVVRALWETHVKS-TVWQKKEAESLEKSALEKTKEEWNPEAKYRRKGIPR<ALY<CKNSF

Parental  IDTNVRLLDKIERNALTRQSSLPKDRGKRSSAFVFELSGEHWTELPDSLKEQTHLREWHISNTLIQIIPT
          .DTN..LL.KIERNAL.RQ.SLPKDRGK.SSAFV..LSGEHWTELPD.LK...HL.E.HI..TLIQI.PT
Retrocopy RDTNMWLLEKIERNALIRQRSLPKDRGKWSSAFVSGLSGEHWTELPDLLK--MHLGEQHICDTLIQITPT

Parental  -YIELFQAMRILDLPRNQISHLPAEIGCLKNLKELNVSFNHLKSIPPELGDCE-NLDRLDCSGNLELTEL
          .YIELF..MRI.DLP..QISHLPAEI.CLKNLK.LNVSF..LKSI.PELGD.E.NL.RLDCSGNLE..EL
Retrocopy YYIELFHSMRIQDLPKTQISHLPAEISCLKNLK*LNVSFTYLKSISPELGDGE<NLERLDCSGNLEFIEL

Parental  PF-ELSNLKQVTFVDISANKFSSVPICVLRMS-NLQWLDISNNNLTDLPQDIDRLEELQSFLLYKNKLTY
          PF..LSN.K.V.FVD...NKF..VPICVLRMS..LQWLDIS.NNLTDL.QD.DRL.ELQ.FLLYK.KLTY
Retrocopy PF>GLSNWKPVAFVDTYTNKFFTVPICVLRMS<YLQWLDIS-NNLTDLTQDRDRLGELQGFLLYKIKLTY

Parental  LPYSMLNLKKLTLLVVSGDHLV
          LPY..LNLK..TLLVV.GDHLV
Retrocopy LPYHELNLKEHTLLVVNGDHLV

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	0.02 RPM
SRP051959_heart	0.00 RPM	33.98 RPM
SRP051959_kidney	0.02 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.39 RPM
SRP051959_lung	0.00 RPM	0.10 RPM
SRP051959_lymph_node	0.07 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.02 RPM	61.71 RPM
SRP051959_spleen	0.06 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2714 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2714 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002149	1 retrocopy	retro_cjac_2714 ,
Homo sapiens	ENSG00000163827	1 retrocopy	retro_hsap_2346,
Gorilla gorilla	ENSGGOG00000004427	1 retrocopy	retro_ggor_1782,
Pongo abelii	ENSPPYG00000013932	1 retrocopy	retro_pabe_2124,
Pan troglodytes	ENSPTRG00000014852	1 retrocopy	retro_ptro_1718,