RetrogeneDB ID: retro_cjac_1956

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:129355808..129356467(-)
• Located in intron of: ENSCJAG00000019786

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD18
• Ensembl ID: ENSCJAG00000031173
• Aliases: None
• Description: potassium channel tetramerization domain containing 18 [Source:HGNC Symbol;Acc:26446]

Sequence

>retro_cjac_1956
AAAAGCCACAAGGCAGAAGAAGAGGTGCCAGATATTCTTCAACTGAACGTAGGTGGCTGTATTTACACAGCCTAGCAGGA
GTCCTTGTGCCGCCTTAAAGACTCCACATTGCCATCTATGTTCAGTGGTTGCTTTCCTCTAAAAACAGATGAGTCAGGGG
CTTGTGTTAATGATTGTGATAGGCATGTATTTAAATACCTTTTGGATTACCTTCATGGCTAAGTTCAGATTCCCATAGAT
GAGCAAGCCCTCATTGCCCTACAAGAAGCAGCTGATTTATTTGGCGTCCCTTATCTGTATAGCCTATCTGACCACTTGGC
CAATGAAATGGAGACATATACTTTAAGGTCAAATACAGACCTTAAAAACACTTTAACAGCCTTCTGTGATTCATATGGTT
TGGTTTACAATAAACCAACAGTTTGGATTCTCAACCATCTTAACAATCTGGTGCAAGCTGTGAGAATAGAATTATTGGTT
TATATGCCACAAAAACTGATAGAACAGATGCTATTGATAAGCAGCTGGGAGGAAGAATTCACAGTAAAAGTATGTTTAAA
AGAGAGGTGGGAAATAATGTTCAGTACATTTGGAGTTATTACTCAGCAGTAGAGTTGAAGAAAATGATGGATGCCTTTGA
TGCTTGGGAAGGAAAAGGT

Alignment

ORF - retro_cjac_1956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.64 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGHEAEEEVLDILRLNVGGCVYTARRESLCRFKDSMLASMFSGRFPLKTDESGACVIDRDGRLFKYLLDY
          ..H.AEEEV.DIL.LNVGGC.YTA..ESLCR.KDS.L.SMFSG.FPLKTDESGACV.D.D...FKYLLDY
Retrocopy KSHKAEEEVPDILQLNVGGCIYTA*QESLCRLKDSTLPSMFSGCFPLKTDESGACVNDCDRHVFKYLLDY

Parental  LHGEVQIPTDEQTRIALQEEADYFGIPYPYSLSDHLANEMETYSLRSNIELKKALTDFCDSYGLVCNKPT
          LHG.VQIP.DEQ..IALQE.AD.FG.PY.YSLSDHLANEMETY.LRSN..LK..LT.FCDSYGLV.NKPT
Retrocopy LHG*VQIPIDEQALIALQEAADLFGVPYLYSLSDHLANEMETYTLRSNTDLKNTLTAFCDSYGLVYNKPT

Parental  VWVLHYLNT-SGASCESRIIGVYATKNDGTDAIDKQLGGRIHSKSIFKREAGNNVQYIWSYYSVAELKKM
          VW.L..LN..SGASCE.RIIG.YATK.D.TDAIDKQLGGRIHSKS.FKRE.GNNVQYIWSYYS..ELKKM
Retrocopy VWILNHLNN<SGASCENRIIGLYATKTDRTDAIDKQLGGRIHSKSMFKREVGNNVQYIWSYYSAVELKKM

Parental  MDAFDAWEGKG
          MDAFDAWEGKG
Retrocopy MDAFDAWEGKG

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	0.35 RPM	1.62 RPM
SRP051959_heart	0.16 RPM	1.07 RPM
SRP051959_kidney	0.38 RPM	1.24 RPM
SRP051959_liver	0.24 RPM	1.10 RPM
SRP051959_lung	0.37 RPM	1.92 RPM
SRP051959_lymph_node	0.66 RPM	2.33 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.48 RPM
SRP051959_spleen	0.55 RPM	1.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1956 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1956 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031173	2 retrocopies	retro_cjac_1956 , retro_cjac_3169,
Otolemur garnettii	ENSOGAG00000012335	1 retrocopy	retro_ogar_3268,
Tarsius syrichta	ENSTSYG00000008420	2 retrocopies	retro_tsyr_293, retro_tsyr_896,