RetrogeneDB ID: retro_cjac_1153

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:52656126..52656705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDC3L
• Ensembl ID: ENSCJAG00000009947
• Aliases: None
• Description: KH domain containing 3-like, subcortical maternal complex member [Source:HGNC Symbol;Acc:33699]

Sequence

>retro_cjac_1153
ATGGACACTCCCAGACGGTTTCCGACGCTCGTGCAACAGATGCAGCCAAAAGCAATGTCATTCGAGGTACTCGGTCAGCT
CCCCAAGAAGTTCTGGTTCCACTCTGAGTTTCTGAAGAATCCGAAGGTAGTTCACCTTAAGGTTTGGCTGGTGGAAAAGA
TCTTCTGCAGAGGCGGAGAGCGCATCCCACAAGTCCAAGGTCTGTCCTAAATCCTGATTCACGTGAATCACTTGGACCCC
AGCAGCGAGGCTGAGATCTTGATATTTGGGAGGCCTTCTTACCAGGAGGACACAATCAAGATGATTGTGAACTTGGCTGA
CTATCACCGCCAGCTCCAGGCGAAAGGCTCAGGAAAGGCCCTCGCCCAGGATGTAGCCACTCAGAAGGCTCAAACCCAGC
GGTCTTCAATAGATGCCTGGGAAGCCGGGACCCAGAGTTCGGTGGAGGTCCGGGAGGTCGGGACACAGGGTTCTCCGGTG
GAGGTGCGGGAGGCCGGGAGCCAGCAGTCCCTCAAGGCTGCCGGTGAGTCGAGGACCCAGCGATCTCCCGAAGCTGCCAG
CAAGGCACGGATCCAGCAG

Alignment

ORF - retro_cjac_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 88.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTPRRFPTLVQLMQPKAMSFEVLGQLPKQFSWFHSEFLKNPKVVRLEVWLVEKIFGRGGERIPQVQGLS
          MDTPRRFPTLVQ.MQPKAMSFEVLGQLPK.F.WFHSEFLKNPKVV.L.VWLVEKIF.RGGERIPQVQGLS
Retrocopy MDTPRRFPTLVQQMQPKAMSFEVLGQLPKKF-WFHSEFLKNPKVVHLKVWLVEKIFCRGGERIPQVQGLS

Parental  QILIHVNHLDPSGEAEILIFGRPSYQEDTIKMIVNLADYHRQLQAKGSGKALAQDIATQKAETQRSSIEV
          .ILIHVNHLDPS.EAEILIFGRPSYQEDTIKMIVNLADYHRQLQAKGSGKALAQD.ATQKA.TQRSSI..
Retrocopy *ILIHVNHLDPSSEAEILIFGRPSYQEDTIKMIVNLADYHRQLQAKGSGKALAQDVATQKAQTQRSSIDA

Parental  REAGTQRSVEVREAWTQRS-VEVREVGTQGSPVEVREAGTQQSLKAASESGTQR
          .EAGTQ.SVEVRE..TQ.S.VEVRE.G.Q.S.....E..TQ.S..AAS....Q.
Retrocopy WEAGTQSSVEVREVGTQGSPVEVREAGSQQSLKAAGESRTQRSPEAASKARIQQ

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	0.07 RPM
SRP051959_heart	0.00 RPM	0.77 RPM
SRP051959_kidney	0.00 RPM	0.13 RPM
SRP051959_liver	0.00 RPM	0.06 RPM
SRP051959_lung	0.00 RPM	0.07 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.20 RPM
SRP051959_spleen	0.00 RPM	0.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1153 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007887	1 retrocopy	retro_amel_1880,
Callithrix jacchus	ENSCJAG00000009947	1 retrocopy	retro_cjac_1153 ,
Callithrix jacchus	ENSCJAG00000009962	1 retrocopy	retro_cjac_3033,
Myotis lucifugus	ENSMLUG00000004469	1 retrocopy	retro_mluc_2196,
Ochotona princeps	ENSOPRG00000013565	3 retrocopies	retro_opri_322, retro_opri_406, retro_opri_651,
Sorex araneus	ENSSARG00000003714	1 retrocopy	retro_sara_631,