RetrogeneDB ID: retro_cjac_2165

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:107176888..107177799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSCJAG00000015859
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_cjac_2165
CTCGTCGCTGGTGGGGCAGACTGCAATGCCTGTGTCTGGAGTTAGGAAGATGCTGTTTGGAAGTCAACCCTGGTGCTCCT
GAGAATTAACTGTGCAGCTACTTTGTGAAGTGGTCCCTCCTAGAGAAAAACTTTTGGTGGGAAGTGGGGCATGACTCATT
TCTGTTTGTTACTGTGAGTCTGAAAATGACTGGTGGGTGAGCAAGCACATTAAAAAGCCAATTTGCTCCACAGTCCTCAG
CTTGGATTGGCATCCCGACAACGTTTTGCTGGCAGCAGGATCAAGTCATTTCAGATGCAGAGTGTTTTCTGCCTACATTA
AAGAAGCGGTTGAAAAGCCAGCCAGCACACCCTGAGGCAGCAAGATGCCTTTTGGGCAGCTGATGTCAGAGTTTGGTGGC
AGTGGCACTGGTGGCTGGGTCCACAGGGTCAGCTTCTCTGCCAGTGAGAGCCACCCGGCCTGGATCAGCCATGATAGTAC
CATGTCTGTTGCTGATGCCTCCAAAAGTGTGTAGGTCTCAACTCTGAAGACAGAGTTCCCGTGGTTCCTGAGTGTGTCAT
TTGTCTCAGAGAACAGCGTCGTGGCTGCTGACCATGACTGCTGTTCAATGCTCTTTAATGATCAAGGCTGCTTGACCTTC
ATCTCCAAGTTAGAAATGGACATTCCAAAACAGAGCATCCAACGCAACTTGTCTGCCACAGAATGCTTCCGCAACATGGA
CAAGAAGGCCATGACTGAGGACCGAAACAACGGCCTTGGAGACCCTGAACCTGAATAGCATCACTTAAGTCTCTATGTAT
GAGGTGGAAAAGCAAGATTGTCGCAAATTTTGCGCTACTGGCATGGATGGAGCCATGGCAATTTGGGATTTCAAGACCCT
CAACTCTTCCATCCAGGGCCTCCGGATAATG

Alignment

ORF - retro_cjac_2165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.26 %
• Parental protein coverage: 75.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IVTCGADRNAYVWSQKDGIWKPTLVILRINRAAT-FVKWSPLENKF-AVGSGARLISVCYFESENDWWVS
          .V..GAD.NA.VWS..D..WK.TLV.LRIN.AAT.FVKWS.LE..F..VGSGA.LISVCY.ESENDWWVS
Retrocopy LVAGGADCNACVWS*EDAVWKSTLVLLRINCAAT<FVKWSLLEKNF<LVGSGA*LISVCYCESENDWWVS

Parental  KHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTG
          KHIKKPI.STVLSLDWHP.NVLLAAGS..F.CRVFSAYIKE..EKPASTP.GSKMPFGQLMSEFGGSGTG
Retrocopy KHIKKPICSTVLSLDWHPDNVLLAAGSSHFRCRVFSAYIKEAVEKPASTP*GSKMPFGQLMSEFGGSGTG

Parental  GWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNY
          GWVH.VSFSAS.S..AW.SHDST.SVADASKSV.VSTLKTEF...LSVSFVSENSVVAA.HDCC.MLFN.
Retrocopy GWVHRVSFSASESHPAWISHDSTMSVADASKSV*VSTLKTEFPWFLSVSFVSENSVVAADHDCCSMLFN-

Parental  DDRGCLTFVSKL--DIPKQSIQRNMSAMERFRNMDKRATTEDRN-TALETLHQNSITQVSIYEVDKQDCR
          .D.GCLTF.SKL..DIPKQSIQRN.SA.E.FRNMDK.A.TEDRN.TALETL..NSIT.VS.YEV.KQDCR
Retrocopy -DQGCLTFISKLEMDIPKQSIQRNLSATECFRNMDKKAMTEDRN>TALETLNLNSIT*VSMYEVEKQDCR

Parental  KFCTTGIDGAMTIWDFKTLESSIQGLRIM
          KFC.TG.DGAM.IWDFKTL.SSIQGLRIM
Retrocopy KFCATGMDGAMAIWDFKTLNSSIQGLRIM

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	48.35 RPM
SRP051959_heart	0.00 RPM	22.91 RPM
SRP051959_kidney	0.00 RPM	25.87 RPM
SRP051959_liver	0.00 RPM	28.98 RPM
SRP051959_lung	0.00 RPM	33.19 RPM
SRP051959_lymph_node	0.00 RPM	20.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.69 RPM
SRP051959_spleen	0.00 RPM	24.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2165 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165 , retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,