RetrogeneDB ID: retro_cjac_574

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82828295..82829256(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM165
• Ensembl ID: ENSCJAG00000018339
• Aliases: None
• Description: transmembrane protein 165 [Source:HGNC Symbol;Acc:30760]

Sequence

>retro_cjac_574
GCCGCGGCCCCGGGCAACAGCCGCGCATCGGCGCCCAGGCCGCTTCTGCTCTTGCTGGTTCAGCTACTGTGGGCCCCGGC
TGGGGTCCGGGCGGGTCCGGATGAAGACCTTAGCCACCGGAACAAAGAACCGCTGGCGCCTGCCCAGCAGCTGCAGTAGC
AGCCGGTGGCCGTGCAGGGCCCCGAGCCGGCCCGGGTTGAGAAAGCATTTACACCAGCAGCTCCAGTTCATACCAATAAG
GAAGATCCTGCTGCCCAAACTGATTTGGGCTTTATGCATGCATTTGTCGCTGCCATATCAGTTGTCATTGTATCTGAATT
GGGTGATAAGACATTTTTTACAGCAACCATCATGGCAATGCGCTATAACCGCCTAACCGTTCTGGCTGGTGCAATGCTTG
CCTTGGGACTAATGACGTTCTTGTCAGTTTTGTTTGGCTATGCCACCACAGTCATCCCCAGGGTCTATACATACTATGTT
TCAACTGTGTTATTTGCCATTTTTGGCATTAGAATGCTGCGGGAAGGCTTGAGGATGAGCCCTGAGGAAAGTCAAGAGAA
ACTGGAAGAAGTTCAGGCTGAATTAAAGAAAAAACATGAAGAATTTCAACAAACCAAACTTTTAAATGGACCAGGAGATG
TCGAAACAGGAACAAGCACAATAGTACCTCAGAAAAAGTGGTTGCATTTTATTTCACCCATTTTTGTTCAAGCTCTTACA
TTAACATTCTTAGCAGAATGGGGTGATCGCTCTCAACTACAATTGTATTGGCAGCAAGAGAGGACCCCTATGGTGTAGCC
GTGGGTGAACCATGGGGCACTCCCTGTGCACGGGACTGGCAGTAATTGGAGGAAGAATGATAGCACAGAAAATCTCTGTC
AGAACTATGACAATCATTGGAGGCATCGTGTTTTTGGCGTTTGCATTTTCTGCATTATTTATAAGCCCTGATTCTGGTTT
T

Alignment

ORF - retro_cjac_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.98 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAPGNSRASAPRLLLLLLVPLLWALAGVRAGPDEDLSHRNKEPPAPAQQLQQQPVAVQGPEPARVEKAF
          AAAPGNSRASAPR.LLLLLV.LLWA.AGVRAGPDEDLSHRNKEP.APAQQLQ.QPVAVQGPEPARVEKAF
Retrocopy AAAPGNSRASAPRPLLLLLVQLLWAPAGVRAGPDEDLSHRNKEPLAPAQQLQ*QPVAVQGPEPARVEKAF

Parental  TPAAPVHTNKEDPAAQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIMAMRYNRLTVLAGAMLALGLMTC
          TPAAPVHTNKEDPAAQT.LGF.HAFVAAISV.IVSELGDKTFF.A.IMAMRYNRLTVLAGAMLALGLMT.
Retrocopy TPAAPVHTNKEDPAAQTDLGFMHAFVAAISVVIVSELGDKTFFTATIMAMRYNRLTVLAGAMLALGLMTF

Parental  LSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLKMSPDEGQEELEEVQAELKKKDEEFQRTKLLNG
          LSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGL.MSP.E.QE.LEEVQAELKKK.EEFQ.TKLLNG
Retrocopy LSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLRMSPEESQEKLEEVQAELKKKHEEFQQTKLLNG

Parental  PGDVETGTSTIVPQKKWLHFISPIFVQALTLTFLAEWGDRSQL-TTIVLAAREDPYGVAVGG-TVGHSLC
          PGDVETGTSTIVPQKKWLHFISPIFVQALTLTFLAEWGDRSQL.T....AAREDPYGVAVG..T.GHSLC
Retrocopy PGDVETGTSTIVPQKKWLHFISPIFVQALTLTFLAEWGDRSQL<TIVL-AAREDPYGVAVGE<TMGHSLC

Parental  TGLAVIGGRMIAQKISVRTVTIIGGIVFLAFAFSALFISPDSGF
          TGLAVIGGRMIAQKISVRT.TIIGGIVFLAFAFSALFISPDSGF
Retrocopy TGLAVIGGRMIAQKISVRTMTIIGGIVFLAFAFSALFISPDSGF

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	0.07 RPM	22.92 RPM
SRP051959_heart	0.07 RPM	11.65 RPM
SRP051959_kidney	0.02 RPM	16.99 RPM
SRP051959_liver	0.02 RPM	8.06 RPM
SRP051959_lung	0.03 RPM	21.12 RPM
SRP051959_lymph_node	0.09 RPM	19.52 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.74 RPM
SRP051959_spleen	0.08 RPM	22.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_574 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_574 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
Callithrix jacchus	ENSCJAG00000018339	1 retrocopy	retro_cjac_574 ,
Ictidomys tridecemlineatus	ENSSTOG00000025897	1 retrocopy	retro_itri_837,