RetrogeneDB ID: retro_cjac_3964

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286436.1:239244..239921(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000020510
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: USP12P1
• Ensembl ID: ENSCJAG00000019344
• Aliases: USP12P1, USP12
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:F7FL24]

Sequence

>retro_cjac_3964
TTGGAAATGCTAATGCCAGTCTCCAAATTCTCCTCCATCTGTACCACGAGAGCCCAAGCTCCGGCATTAGAGAAAAAGAT
TGGTCCAGAACAGTTTCCAGTCAATGAGCACTATTTTGGACGAGTCAATTTTGGGAACACTTGCTACTGCAATTCAGTTC
TTCAAGCACTTTATTTTTGTCGTCCATTTCGGGAAAAAGTTCTTCCATATAAGGGTCAACCTAGGAAAATGGAGAACCTT
CTTACATGCTTAGCAGATCTCTTCCATAGCACAGCCGCTCAGAAGAAAAAGGTTGGAGTAATACCTCCCAAGAAGTTCAT
CACAAGATTACGGAAAGAAAATGAGCTTTTTGACAACGACATGCAGCAAGATCCCATGAATTCTTAAATTATCTACTAAA
CACAATTGCTGTTATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTCACTTACCTAATGGTAATATTGATGATG
AAAATAATAACAGTGCACCAGACCCAAAGTGGGTTCATGAGATTTTTCAGGGAACATTAACTAATGAAACCACATGTGTT
ACTTATGAAACTACAGGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACTTGGAACAAAATGCATCAATCACTCA
CTGCTTAAAAGGTTTCAGCAACAGGGAAACTCTATGC

Alignment

ORF - retro_cjac_3964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY
          .E.LM.VSKF.SICT..A.A.ALEK.IGPEQFPVNEHYFG.VNFGNTCYCNSVLQALYFCRPFREKVL.Y
Retrocopy LEMLMPVSKFSSICTTRAQAPALEKKIGPEQFPVNEHYFGRVNFGNTCYCNSVLQALYFCRPFREKVLPY

Parental  KSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQD-AHEFLNYLLNTIADI
          K.QPRK.E.LLTCLADLFHS.A.QKKKVGVIPPKKFITRLRKENELFDN.MQQD..HEFLNYLLNTIA.I
Retrocopy KGQPRKMENLLTCLADLFHSTAAQKKKVGVIPPKKFITRLRKENELFDNDMQQD<SHEFLNYLLNTIAVI

Parental  LQEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQN
          LQEERKQEKQNG.LPNGNID.ENNNS.PDP.WVHEIFQGTLTNET.C.T.ET..SKDEDFLDLSVD.EQN
Retrocopy LQEERKQEKQNGHLPNGNIDDENNNSAPDPKWVHEIFQGTLTNETTCVTYETTGSKDEDFLDLSVDLEQN

Parental  TSITHCLRGFSNTETLC
          .SITHCL.GFSN.ETLC
Retrocopy ASITHCLKGFSNRETLC

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	58.04 RPM
SRP051959_heart	0.00 RPM	52.78 RPM
SRP051959_kidney	0.02 RPM	54.11 RPM
SRP051959_liver	0.00 RPM	39.70 RPM
SRP051959_lung	0.00 RPM	46.79 RPM
SRP051959_lymph_node	0.00 RPM	30.82 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.44 RPM
SRP051959_spleen	0.00 RPM	35.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3964 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3964 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3964 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964 , retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,