RetrogeneDB ID: retro_cjac_3022

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:127680273..127681040(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001806
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR82P1
• Ensembl ID: ENSCJAG00000006114
• Aliases: WDR82P1, WDR82
• Description: None

Sequence

>retro_cjac_3022
AGGAGGGCAAACCAAAGAAAACCTGTTCAGTACCAAATATGGCGTGGACCTCATGCGGCAAACACAGTTGTTTGCTCTCA
CATAATCGATGATACTATTGGTTACTTCTCTTCACATGACAATAAATACATTAGATACTTTCCTGGACATAGCCAAAGGG
TGGTGGCCTTGTCCATGTCACCTGCGGATGATGCTTTAATTTCTGGGTCTCTTGCTAAGACCGTTCGACTCTGGGATCTC
TGGTCTCCTAACTGCAAGGGCCTCATGCATCTACAGCGGAAGCCAGTTTGTTCTTCGGATCCAGAAGGGTTAATTTTCGC
TGCCGGTGTCAACTCTGAAAAGGTCAAACTTTATGACCTTTGTTCTTTCCATAAGGGGCCATTTGCTACCTTTAAGATGC
AGTACGGTCGAACTTGTGAGTGGACAGGACTTCAGGTCAGCAAGGATGGCAAACTCATCCTCATTTCCACCAATGGCAGC
TTCATTCCTCTACTTGAAGCATTCAAGGGAGGGGTGATGCACACGTTGGGGGGTTATGCCAACAGCAAAGCTGTCACACT
ACAGGCTTCGTTTACTCCAGACTCTCAGTTTATTATGATTGGTTCAGAGGATGGCAAGACCATGTCTGGAATGGAGAGAG
ATGTATAAAAGTAGCTGTGTTGGATGGTAAACACACAGGCCCAATTACCTGTTGGCAATTCAACCCCAAGTTCATGACTT
TTGCCAGTGCATGTTCCAACATGGCCTTCTGGTTGCCCACCATTGAT

Alignment

ORF - retro_cjac_3022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 82.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRTLYSKKYGVDLIRYTHAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVALSMSPVDDTFISG
          .R....K.......R..HAANTVV..S..IDDTI.Y.S.HDNKYIRYFPGHS.RVVALSMSP.DD..ISG
Retrocopy RRANQRKPVQYQIWRGPHAANTVV-CSHIIDDTIGYFSSHDNKYIRYFPGHSQRVVALSMSPADDALISG

Parental  SLDKTIRLWDLRSPNCQGLMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTC
          SL.KT.RLWDL.SPNC.GLMHLQ.KPVCS.DPEGLIFAAGVNSE.VKLYDL.SF.KGPFATFKMQY.RTC
Retrocopy SLAKTVRLWDLWSPNCKGLMHLQRKPVCSSDPEGLIFAAGVNSEKVKLYDLCSFHKGPFATFKMQYGRTC

Parental  EWTGLKFSNDGKLILISTNGSFIRLIDAFKGVVMHTFGGYANSKAVTLEASFTPDSQFIMIGSEDGKI-H
          EWTGL..S.DGKLILISTNGSFI.L..AFKG.VMHT.GGYANSKAVTL.ASFTPDSQFIMIGSEDGK..H
Retrocopy EWTGLQVSKDGKLILISTNGSFIPLLEAFKGGVMHTLGGYANSKAVTLQASFTPDSQFIMIGSEDGKT<H

Parental  VWNGESGIKVAVLDGKHTGPITCLQFNPKFMTFASACSNMAFWLPTID
          VWNGE..IKVAVLDGKHTGPITC.QFNPKFMTFASACSNMAFWLPTID
Retrocopy VWNGERCIKVAVLDGKHTGPITCWQFNPKFMTFASACSNMAFWLPTID

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	22.61 RPM
SRP051959_heart	0.05 RPM	30.31 RPM
SRP051959_kidney	0.09 RPM	26.71 RPM
SRP051959_liver	0.00 RPM	22.55 RPM
SRP051959_lung	0.02 RPM	33.85 RPM
SRP051959_lymph_node	0.00 RPM	39.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.27 RPM
SRP051959_spleen	0.00 RPM	33.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3022 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3022 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_419
Pongo abelii	retro_pabe_300
Macaca mulatta	retro_mmul_511

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022 ,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,