RetrogeneDB ID: retro_cjac_2781

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:158031341..158031804(+)
• Located in intron of: ENSCJAG00000006087

Retrocopy information

• Ensembl ID: ENSCJAG00000006116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KCTD2
• Ensembl ID: ENSCJAG00000014605
• Aliases: None
• Description: None

Sequence

>retro_cjac_2781
CAGGCTAACACCGACAAGGAGGAAATCTTCGCCCATTTAATAGGCAAAGACTGCACCTGTTTTGGGCCTGCACTGAACCA
CCTGAGACATGGCAAGACGGTGATTAGCAAAGACATTGCGGAGGAAGGAGTGTTGGAAAAAGCAGAATTTTACGACATGA
CCTCATTAATAAAACTTGTAAAGGACAAAATTAGAGAACAAGAGAGCAAAGCCTCACAGGTGCCGTGAAGCATGTGTCCG
GTGTGCTTCAGTGCCCAGAGGGGCTCACACAGGTGGTGCCCAGCATGTCCGCTGGCTGAAGTTTGAACAACTGGGCAGCT
TTGACTCCTCTTACAACTATGGGGATGCAGACCGGGCCAAGTTCCCCTGTGTGCTGTCCAGGGAGCTTCGCAGCACCCCA
TACAGTATGGCCAGCAGGCCCAGCAAGAAGGCCAGGATTTTGCAAGAATGAGGTTCAAGGATA

Alignment

ORF - retro_cjac_2781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.96 %
• Parental protein coverage: 65.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELDSDKDETGAYLIDRDPTYFGPILNYLRHGKLIITKELAEEGVLEEAEFYNIASLVRLVKERIRDNENR
          ....DK.E..A.LI..D.T.FGP.LN.LRHGK..I.K..AEEGVLE.AEFY...SL..LVK..IR..E..
Retrocopy QANTDKEEIFAHLIGKDCTCFGPALNHLRHGKTVISKDIAEEGVLEKAEFYDMTSLIKLVKDKIREQESK

Parental  TSQ-GPVKHVYRVLQCQEEELTQMVSTMSDG-WKFEQLISIGSSYNYGNEDQAEFLCVVSRELNNSTNGI
          .SQ.G.VKHV..VLQC..E.LTQ.V..MS.G..KFEQL.S..SSYNYG..D.A.F.CV.SREL.......
Retrocopy ASQ<GAVKHVSGVLQC-PEGLTQVVPSMSAG<LKFEQLGSFDSSYNYGDADRAKFPCVLSRELRSTPYSM

Parental  VIEPSEKAKILQERGSRM
          ...PS.KA.ILQE.GSR.
Retrocopy ASRPSKKARILQE*GSRI

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	0.22 RPM	4.59 RPM
SRP051959_heart	0.21 RPM	5.77 RPM
SRP051959_kidney	0.64 RPM	6.72 RPM
SRP051959_liver	0.06 RPM	3.60 RPM
SRP051959_lung	0.20 RPM	7.08 RPM
SRP051959_lymph_node	0.07 RPM	5.84 RPM
SRP051959_skeletal_muscle	0.20 RPM	4.19 RPM
SRP051959_spleen	0.15 RPM	5.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2781 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2781 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	ENSBTAG00000021231	1 retrocopy	retro_btau_927,
Callithrix jacchus	ENSCJAG00000014605	1 retrocopy	retro_cjac_2781 ,
Echinops telfairi	ENSETEG00000013965	1 retrocopy	retro_etel_643,
Pongo abelii	ENSPPYG00000008616	1 retrocopy	retro_pabe_2093,
Pan troglodytes	ENSPTRG00000009629	1 retrocopy	retro_ptro_1685,