RetrogeneDB ID: retro_cjac_3065

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:39449725..39450249(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005302
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPRKB
• Ensembl ID: ENSCJAG00000004162
• Aliases: None
• Description: TP53RK binding protein [Source:HGNC Symbol;Acc:24259]

Sequence

>retro_cjac_3065
ATGCAGTTAACACATCATCTGGACCTATTTCCTAAATGCAGGGTGACCTTTCTGTTATTTAAAGATGTCAAAAATGCAGG
AGACTTGAGAAGGAAGGCCATGGAAGGGAACATCGATGGATCACTGATAAATTTTACAGTGATTGTGGATCCAGTACAGA
TACCTGTGGCAGCAAATAAAGCAGTTCACCTCTACAAACTGGGAAAAATGAAGACAAGAACTCTATCTACTGAAATTATG
TACAACCTTTCCCCAAATAACAATATTTCAGAGGCTTTGAAAAAAATTGGTATCTCAGTAAATGACACTTCAATTCTAAT
TGTTTACATTGAAGAGGGAGAAAAACAAATAAATCAAGAATACCTGATATCTCAAATAGAAGGTCATCAGGTTTCTCTGG
AAAACCTTCCTGAAATAACAAAAATTACAGAAGTCAAAAAGATATATAAACTTTCTTCACAAGAAGAAAGTATTGTGACA
TTATTGGATGGTGTCATTGTAGAATGTCAACAAAAGATGTTTTG

Alignment

ORF - retro_cjac_3065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQLTHQLDLFPECRVTLLLFKDVKNAGDLRRKAMEGTIDGSLINPTVIVDPFQILVAANKAVHLYKLGKM
          MQLTH.LDLFP.CRVT.LLFKDVKNAGDLRRKAMEG.IDGSLIN.TVIVDP.QI.VAANKAVHLYKLGKM
Retrocopy MQLTHHLDLFPKCRVTFLLFKDVKNAGDLRRKAMEGNIDGSLINFTVIVDPVQIPVAANKAVHLYKLGKM

Parental  KTRTLSTEIIYNLSPNNNISEALKKFGISGNDTSILIVYIEEGEKQINQEYLISQVEGHQVSLENLPEIT
          KTRTLSTEI.YNLSPNNNISEALKK.GIS.NDTSILIVYIEEGEKQINQEYLISQ.EGHQVSLENLPEIT
Retrocopy KTRTLSTEIMYNLSPNNNISEALKKIGISVNDTSILIVYIEEGEKQINQEYLISQIEGHQVSLENLPEIT

Parental  NITEVKKIYKLSSQEERIGTLLDGII-CRMSTKDVL
          .ITEVKKIYKLSSQEE.I.TLLDG.I.CRMSTKDVL
Retrocopy KITEVKKIYKLSSQEESIVTLLDGVI<CRMSTKDVL

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	5.99 RPM
SRP051959_heart	0.00 RPM	6.51 RPM
SRP051959_kidney	0.02 RPM	4.88 RPM
SRP051959_liver	0.04 RPM	5.96 RPM
SRP051959_lung	0.00 RPM	3.38 RPM
SRP051959_lymph_node	0.00 RPM	4.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.02 RPM
SRP051959_spleen	0.02 RPM	4.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3065 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3065 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012021	1 retrocopy	retro_chof_35,
Callithrix jacchus	ENSCJAG00000004162	3 retrocopies	retro_cjac_1999, retro_cjac_2867, retro_cjac_3065 ,
Homo sapiens	ENSG00000144034	1 retrocopy	retro_hsap_552,
Gorilla gorilla	ENSGGOG00000009062	1 retrocopy	retro_ggor_501,
Macaca mulatta	ENSMMUG00000030805	1 retrocopy	retro_mmul_1571,
Monodelphis domestica	ENSMODG00000016950	2 retrocopies	retro_mdom_1264, retro_mdom_465,
Nomascus leucogenys	ENSNLEG00000000300	2 retrocopies	retro_nleu_2021, retro_nleu_957,
Oryctolagus cuniculus	ENSOCUG00000016251	2 retrocopies	retro_ocun_519, retro_ocun_769,
Otolemur garnettii	ENSOGAG00000032893	2 retrocopies	retro_ogar_523, retro_ogar_849,
Pongo abelii	ENSPPYG00000012292	1 retrocopy	retro_pabe_509,
Pteropus vampyrus	ENSPVAG00000012419	1 retrocopy	retro_pvam_75,
Ictidomys tridecemlineatus	ENSSTOG00000016406	4 retrocopies	retro_itri_1613, retro_itri_453, retro_itri_918, retro_itri_919,
Tupaia belangeri	ENSTBEG00000014584	2 retrocopies	retro_tbel_33, retro_tbel_3630,
Vicugna pacos	ENSVPAG00000007934	2 retrocopies	retro_vpac_149, retro_vpac_192,