RetrogeneDB ID: retro_ptro_2460

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:103415456..103416259(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSPTRG00000000136
• Aliases: None
• Description: None

Sequence

>retro_ptro_2460
ATATCTGCATGTATTCAGGTAACTAGAGACAAGAATTATGAGCCCATTGAAATACCATCAGAAGATGATAGAACAGTGCT
GCTGCCCATGGTTACAGTCCAGTTTCCAGGGGCATGTGGGCTCCCCTACAGGATTCCAGTGTCTCAGGTATTAGGAGTGT
CTGCTGGTAGAAGGAATTCTGCATGCCCCCAGTGCTGGCTGGGGAAATTTGGTGTATGTTGTCAACTATTCTGTAGATAA
CTACAGAAAAAGGGAAAAGACAGATACTTCATTAGCCATAAAAGTGAAAAGAGCAGTCCAGAAAACATCTGCTTTAGCAG
TGTTGGGTCTCCCATGGAAAACAACTGAACAGGATCTGAAAGAATATTTCAGTACCTTTGGAGAAATTCTTATGGTTCAG
GTCAAGAAGGATGTTAGAACTGGCTATTCAAAGGGGTTTGGCTTTGTTTATTTTATAAAATATGAAACCCAGGTGAAAGA
ATGTCACAGCAACATAAGACAGATAGATGATGGTGTGACTGTACAGTTCCTAACTCTAAAGCAAACACTGAATGAGACTT
TGAGAAGCAAAAAGATGTTTGTGGGGTGTTGTACAGAGATTATGAATTCTGATAAGCTGCAGCAGTTCTTTGGTCATTGC
AGAGAAGTGATAGATGTCTTCATTTCCAAACCATTCAGGGACTTTGCCTTTCTTACATTGCAGATGATTAGCTTGCCCAG
TCTCTTTGTGGAGAGGACTTGATTATTAAGGGAATCAGCATACATATATCCAGTGCAAGTGTAAGCACAATAGCAATAGA
CAG

Alignment

ORF - retro_ptro_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.53 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVR-LVEGILHAPDAGWG
          .S..I.VT.D.N.EPIEIPSEDD.TVLL..VT.QFPGACGL.YR.PVSQ...GV..LVEGILHAP.AGWG
Retrocopy ISACIQVTRDKNYEPIEIPSEDDRTVLLPMVTVQFPGACGLPYRIPVSQVL-GVS>LVEGILHAPSAGWG

Parental  NLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL
          NLVYVVNY..DN.RK...TD.S.A.KVKRAVQKTS.L.VLGLPWKTTEQDLKEYFSTFGE.LMVQVKKD.
Retrocopy NLVYVVNYSVDNYRKREKTDTSLAIKVKRAVQKTSALAVLGLPWKTTEQDLKEYFSTFGEILMVQVKKDV

Parental  KTGHSKGFGFVRFTEYETQVKV-MSQRHMIDGRWCDCKLPNS-KQSQDEPLRSRKVFVGRCTEDMTEDEL
          .TG.SKGFGFV.F..YETQVK..MSQ.H..D..WCDC..PNS.KQ...E.LRS.K.FVG.CTE.M..D.L
Retrocopy RTGYSKGFGFVYFIKYETQVKE<MSQQHKTDR*WCDCTVPNS>KQTLNETLRSKKMFVGCCTEIMNSDKL

Parental  REFFSQYGDVMDVFIPKPFRAFAFVT-FADDQIAQSLCGEDLIIKGISVHISNA-EPKHNSNRQ
          ..FF.....V.DVFI.KPFR.FAF.T..ADD..AQSLCGEDLIIKGIS.HIS.A...KHNSNRQ
Retrocopy QQFFGHCREVIDVFISKPFRDFAFLT<IADD*LAQSLCGEDLIIKGISIHISSA<KCKHNSNRQ

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	107.44 RPM
SRP007412_cerebellum	0.00 RPM	197.99 RPM
SRP007412_heart	0.00 RPM	100.03 RPM
SRP007412_kidney	0.00 RPM	120.64 RPM
SRP007412_liver	0.00 RPM	95.62 RPM
SRP007412_testis	0.00 RPM	160.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2460 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2460 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3637
Macaca mulatta	retro_mmul_1847
Callithrix jacchus	retro_cjac_2457

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460 , retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,