RetrogeneDB ID: retro_cjac_2365

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:107743946..107744709(+)
• Located in intron of: ENSCJAG00000005955

Retrocopy information

• Ensembl ID: ENSCJAG00000033160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSCJAG00000015849
• Aliases: None
• Description: None

Sequence

>retro_cjac_2365
CGTGTCATCTCCATCAGTTATTTCGAGCAGGAGAATGACTGGTGGGTTTGCAAGCACATCAAGAAGCCCATCCACTCCAC
GGTCCTCAGCCTGGACTGGCACCCCAACAATGTGCTGCTGGCTGCCAGCTCCTGTGACTTCAAGTGCCGGATCTTATCAG
CCTACATCAAGGAGGTGGAGGAGCGGCCGGCACCCACACCATGGGGCTCTAAGACGCCCTCTGGGGAGCTGATGTTTGAG
TCCAGCAGTAGCTGCGGCTGGGTACATGGCGTCTGCTTCTCAGCCAGCGGGAGCCGCTTGGCCTGGGTGAGCCATGACAG
CACCGTGTGCCTGGCTGATGCCGAGAAGAAGATGGCCGTCGCGACCCTGGCCTCTGAAACACTGCCACTGCTGGCGCTGA
CCTTCATCACAGACAAAAGCCTGGTGGCAGCGGGCATGACGGCTTCCCGGTGCTGTTCACCTACAAAGCCGCTGCGGGGA
CGCTGAGCTTTGGTGGGCGGCTGGATGTGCCCAAGCAGAGCTCGCAGCGCGGCTTGATGGCCCGCGAGGCTTCCAAAACC
TTGACAAGAAGGCGAACTCCGAGGGAGGCACCTCCACGGGCTCGGTCCTGGACTCGCTGCACAAGAATAGCGTCAGCCAG
ATCTCGGTGCTCAGCGGGGGCAAGGCCAAGTGCTCACAGTTCTGCACCGGTGGCATGGACGGTGGCATGAGTATCTGGGA
TGTGAAGAGCTTGGAGTCAGTCTTGAAGGACCTCAAGATCAAA

Alignment

ORF - retro_cjac_2365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 68.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVISICYFEQENDWWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWG
          RVISI.YFEQENDWW.VCKHIKKPI.STVLSLDWHPNNVLLAA.SCDFKCRI.SAYIKEVEERPAPTPWG
Retrocopy RVISISYFEQENDWW-VCKHIKKPIHSTVLSLDWHPNNVLLAASSCDFKCRILSAYIKEVEERPAPTPWG

Parental  SKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTLCLADAEKKMAVATLASETLPLLALTFITDN
          SK.P.GELMFESSSSCGWVHGVCFSASGSR.AWVSHDST.CLADAEKKMAVATLASETLPLLALTFITD.
Retrocopy SKTPSGELMFESSSSCGWVHGVCFSASGSRLAWVSHDSTVCLADAEKKMAVATLASETLPLLALTFITDK

Parental  SLVAA-GHDCFPVLFTYDAAAGTLSFGGRLDVPKQSSQRGLTARER-FQNLDKKANSEGSTAAGSGLDSL
          SLVAA.GHD.FPVLFTY.AAAGTLSFGGRLDVPKQSSQRGL.ARE..FQNLDKKANSEG.T..GS.LDSL
Retrocopy SLVAA<GHDGFPVLFTYKAAAGTLSFGGRLDVPKQSSQRGLMAREA<FQNLDKKANSEGGTSTGSVLDSL

Parental  HKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVKSLESALKDLKIK
          HKNSVSQISVLSGGKAKCSQFCT.GMDGGMSIWDVKSLES.LKDLKIK
Retrocopy HKNSVSQISVLSGGKAKCSQFCTGGMDGGMSIWDVKSLESVLKDLKIK

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	1.31 RPM	45.60 RPM
SRP051959_heart	0.86 RPM	14.24 RPM
SRP051959_kidney	0.98 RPM	13.02 RPM
SRP051959_liver	0.65 RPM	24.84 RPM
SRP051959_lung	1.27 RPM	36.96 RPM
SRP051959_lymph_node	1.89 RPM	50.39 RPM
SRP051959_skeletal_muscle	0.70 RPM	5.63 RPM
SRP051959_spleen	1.72 RPM	62.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2365 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2365 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365 ,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,