RetrogeneDB ID: retro_cjac_2734

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:71230010..71230876(+)
• Located in intron of: None

Retrocopy information

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

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_2734
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCATAGTATAGCCACACAGAAGGGAAAGGTTGAAGTAATATCTCC
TGAGAAGTTCAAAACAAGATTAGAGAAAGAAAATGAGCTTTTCTGCATGCAACAAGATGCCCATGGATTCTTAAATTACC
TACTAAATACAATTGCTGATACTTTACAAGAAGAAAGAAGTCAGGATAAACAAAATGATTGCTTACCAAATGGTAATATT
GACACTGAAAATAACAACAGCACTCCGGACACAATGTAGGTTCATGAAATTTTTCAGGAACAATTAACTAATAAAACCAG
ATGTCTTACTTGTGAAACTATAACAGCAAAGATGAAGATTTTAAGGAACTTCCTGTGATGTAGAACAAAATGTATCAGTT
ATTCACTGTTTAAGTGTTTTTTAGCAAGACAGAAACTCTGTGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTAGCA
AACAGGAAGCACACAAATGAATGAATGCTTAAAAACCACCCATGATTCCAGCTCTACATCTGAAAAGATTTAAATGTGTG
GATTAACTTCACTGATGTATGCAACTTTCTTACTAGGTAGTTTTTCATTTAGAACTTTGTCTGTGTAACACTTCCGATGA
TGCAAGTAATCCAGACAGAATCCAGGGCCTTGTGGGTATTATGATTCAATGTGGAAGTGGTCACAGGTAAGGCCATTATA
TTGCAATTTAATGAGTTAAGAAATCAAGATTTCTGCTTGTTGTTTGATGACACTGTAGAAAAAAAAATGAATTGCACAAG
TTACTGAAGAATTCCATGGATTGAAATCAGATTATCTTGAAGAACTCAGAGTCTGGTTACATTCTG

Alignment

ORF - retro_cjac_2734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQ
          ....L.C.A..FHSIATQK.KV.VI.P.KF.TRL.KENELF...MQQDAH.FLNYLLNTIAD.LQEER.Q
Retrocopy RRKILMCSATFFHSIATQKGKVEVISPEKFKTRLEKENELF--CMQQDAHGFLNYLLNTIADTLQEERSQ

Parental  EKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETI-SSKDEDFLDL-SVDVEQNTSITH
          .KQN..LPNGNID.ENNNSTPD...VHEIFQ..LTN.TRCLTCETI..SKDEDF..L.S.DVEQN.S..H
Retrocopy DKQNDCLPNGNIDTENNNSTPDTM*VHEIFQEQLTNKTRCLTCETI<NSKDEDFKEL<SCDVEQNVSVIH

Parental  CLR-GFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLE
          CL...FS.TETL.SEY..YCEEC.SKQEAHK.M...K.PMI.ALHLKRFK..D.LH....LSY.VVF.LE
Retrocopy CLS>FFSKTETL*SEYRHYCEECCSKQEAHK*MNA*KPPMIPALHLKRFKCVD*LH*CMQLSY*VVFHLE

Parental  LRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAI--VKSHDF-WLLFDDDIVEKID-AQAIEEFYG
          L.L.NTS.DA.NPDR...LV.....CGSG...GHYIAI..VK...F..LLFDD....K...AQ..EEF.G
Retrocopy LCLCNTSDDASNPDRIQGLVGIMIQCGSGHR*GHYIAI**VKKSRF>CLLFDDTVEKKMN>AQVTEEFHG

Parental  LTSD-ISKNSESGYIL
          L.SD.I.KNSESGYIL
Retrocopy LKSD>ILKNSESGYIL

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	0.29 RPM	58.04 RPM
SRP051959_heart	0.49 RPM	52.78 RPM
SRP051959_kidney	0.42 RPM	54.11 RPM
SRP051959_liver	0.26 RPM	39.70 RPM
SRP051959_lung	0.46 RPM	46.79 RPM
SRP051959_lymph_node	0.41 RPM	30.82 RPM
SRP051959_skeletal_muscle	0.13 RPM	30.44 RPM
SRP051959_spleen	0.44 RPM	35.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2734 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2734 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2328
Pan troglodytes	retro_ptro_1701
Gorilla gorilla	retro_ggor_1767
Pongo abelii	retro_pabe_2110
Macaca mulatta	retro_mmul_937

---

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,