RetrogeneDB ID: retro_cjac_2055

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:48091588..48092148(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003555
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSCJAG00000010160
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_cjac_2055
CTGGAAGAGCTGAAGGGTCAGGAAGACGAGTTTAATGAGGAGGATGAACGTGCTGTTGAAATGCGCAGACGGCCGAGACT
GGCTGAGCGGAAAGCAGCTAAACTGAAGAATAAATGTGGAGAAGGTTTGGAGATCTCAGGGAAGGCTTATGTCAGGAAGT
AACCAGAGCCGGTGAGGGCTTGTGGGTCATCTTGCACCTTTGCAAACAAGGAATTCCCCTGTGTGCCCTGATAAATGAGC
ACGTCAGTGGACTTGGCAGCAAGTTTCCTGATGTGAAGTTTCTCAAAGCCATCTCAACAACCTGCACACCCAACTACCCT
GATAGGACTCCGCCAGCGATATCTGTTTACCTGGAAGGTGATATCAAGGCTCAGTTTGTCGGTCCTCTGGTGTTTGGTGG
CATGAACCTGACAAGAGATGAGTTGAAGTGGAAACTGTCTGAATCTGGAGCAATTAGGACGGACTTGGAGGAGAACCCTA
AGAAGCAAATTGAAGACGTGTTGCTGTCCTCAGTGCGGCGCTCTGTCCCCACGTGGAGGGACAGCGATTCCGACGGGGAC

Alignment

ORF - retro_cjac_2055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEELKDHEDEFNEEDERAIEMYRRQRLAEWKATKLKNKFGEVLEISGKDYV-QEVTKAGEGLWVILHLYK
          LEELK..EDEFNEEDERA.EM.RR.RLAE.KA.KLKNK.GE.LEISGK.YV.QEVT.AGEGLWVILHL.K
Retrocopy LEELKGQEDEFNEEDERAVEMRRRPRLAERKAAKLKNKCGEGLEISGKAYV<QEVTRAGEGLWVILHLCK

Parental  QGIPLCALINQHLSGLASKFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLTR
          QGIPLCALIN.H.SGL.SKFPDVKF.KAISTTC.PNYPDR..P.I.VYLEGDIKAQF.GPLVFGGMNLTR
Retrocopy QGIPLCALINEHVSGLGSKFPDVKFLKAISTTCTPNYPDRTPPAISVYLEGDIKAQFVGPLVFGGMNLTR

Parental  DELEWKLSESGAVKTDLEENPKKQIEDVLLSSVRRSVPTWRDSDSDGD
          DEL.WKLSESGA..TDLEENPKKQIEDVLLSSVRRSVPTWRDSDSDGD
Retrocopy DELKWKLSESGAIRTDLEENPKKQIEDVLLSSVRRSVPTWRDSDSDGD

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	0.02 RPM	10.38 RPM
SRP051959_heart	0.23 RPM	14.07 RPM
SRP051959_kidney	0.18 RPM	14.22 RPM
SRP051959_liver	0.00 RPM	4.14 RPM
SRP051959_lung	0.15 RPM	8.90 RPM
SRP051959_lymph_node	0.02 RPM	6.89 RPM
SRP051959_skeletal_muscle	0.04 RPM	8.95 RPM
SRP051959_spleen	0.11 RPM	8.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2055 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055 ,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,