RetrogeneDB ID: retro_cjac_1681

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:32075992..32076325(-)
• Located in intron of: ENSCJAG00000009018

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC4
• Ensembl ID: ENSCJAG00000016175
• Aliases: None
• Description: None

Sequence

>retro_cjac_1681
ATGACTGCCACTCTCCGCCCCTATCTGAGTGCCGTGCGGGCCACACTGCAGGCTGCCCTCTGCCTGGAGAACTTCTCCTG
TCAGGTTGTGGAACGACACAACAAGCCGTAAGTGGAAGTCAGGAGTAGCAAAGAACTCCTGTTACAACCCGTGACCATCA
GCAGGAATGAGAAGGAAAAGATTCCGATTGAGGGCTCCATCAACTCTGTCTGGGTCAGCATTGCTGTGAAACAGGCTGAT
GAGATCAAGGAGATTTTATGCCACAAATTCATGCGCTTCATGATGATGTGAGCAGAAAACTTCTTCATCCTTTGAAGGAA
GCCTGTGGAGGGG

Alignment

ORF - retro_cjac_1681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 66.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKVLIEGSINSV
          MTATLRPYLSAVRATLQAALCLENFS.QVVERHNKP.VEVRSSKELLLQPVTISRNEKEK..IEGSINSV
Retrocopy MTATLRPYLSAVRATLQAALCLENFSCQVVERHNKP*VEVRSSKELLLQPVTISRNEKEKIPIEGSINSV

Parental  RVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEG
          .VSIAVKQADEI..ILCHKFMRFMMM.AENFFIL.RKPVEG
Retrocopy WVSIAVKQADEIKEILCHKFMRFMMM*AENFFIL*RKPVEG

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	0.11 RPM	18.28 RPM
SRP051959_heart	0.14 RPM	8.56 RPM
SRP051959_kidney	0.13 RPM	14.20 RPM
SRP051959_liver	0.06 RPM	12.37 RPM
SRP051959_lung	0.11 RPM	15.57 RPM
SRP051959_lymph_node	0.25 RPM	23.04 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.77 RPM
SRP051959_spleen	0.21 RPM	19.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1681 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1681 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007964	2 retrocopies	retro_btau_680, retro_btau_849,
Callithrix jacchus	ENSCJAG00000016175	1 retrocopy	retro_cjac_1681 ,
Myotis lucifugus	ENSMLUG00000025088	1 retrocopy	retro_mluc_2078,
Monodelphis domestica	ENSMODG00000005136	1 retrocopy	retro_mdom_1390,
Otolemur garnettii	ENSOGAG00000026074	2 retrocopies	retro_ogar_1033, retro_ogar_875,