RetrogeneDB ID: retro_cjac_2457

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:101798482..101799277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSCJAG00000002381
• Aliases: None
• Description: TAR DNA binding protein [Source:HGNC Symbol;Acc:11571]

Sequence

>retro_cjac_2457
TCTGAATATATTTAGGTAACAATAGACTAGAATAATGAACCCATTGAAATACCATCAGAAGTCAATGGAATGATGCTTCT
GCCCATGGTTACAGAGGTATGTGGGCTTCCCTACAGGATTCCTATGTCTTGGGTTATTAGAGGTATCTGGCTGGTAGAAG
GAATTCTGCATGGTCCCAATGATGGCTGGGGAAATTTGGTATATGTTGTCAACTATCCCAAAGATAACTAAAGAAGAAGG
GATAAGACAGATGCTTCATTAGCCATAAAAGTGAAAAGAGCAGTCCAGAAAACATCTGACTTAGTAGTGTTGGGTCTCCC
ATGGAAAACAACTGAACAGGATCTGAAAGAATATTTCAGTAGCTTCAGAGAAATACTTATGGTGCAGGTCAAGAAGGATG
TTAGAAGTAGCTATTCAAAGGGGTTTGGCTTTGCTCATTTTATAAAATATGAAACCCAGGTGAAAGAATGTCATAGCAAC
ATAAGACAGATGGATGATGGTGTGACTGTACACTTCCTAATTCTAAGAAAACGCTGAATGAAACTTTGAGAAGTGAAAGG
ATATTTATGGGGTATTGTACAGAGAACATGAATTCTGATAAGCTGCACTAGTTCTTTTGGCAGGACAGAGAAGTGGTAGA
TGTCTTCATTCCCAAACCACTCAGGGCCTTTGCCTTTGTTACATTGCAGATTAATAGCTTGCCCAGTCTCTCAGTGGAGA
GAACTTGATTATTAAAGGAATCAGGATACATATATCCAATGCAGGCATAAGCACAATAGCAATAAACAGAAAGAG

Alignment

ORF - retro_cjac_2457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 65.22 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNL
          SEYI.VT.D.N.EPIEIPSE..G..LL..VT......CGL.YR.P.S...RG..LVEGILH.P..GWGNL
Retrocopy SEYI*VTID*NNEPIEIPSEVNGMMLLPMVTE----VCGLPYRIPMSWVIRGIWLVEGILHGPNDGWGNL

Parental  VYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKDYFSTFGEVLMVQVKKDLKT
          VYVVNYPKDN.R..D.TDAS.A.KVKRAVQKTSDL.VLGLPWKTTEQDLK.YFS.F.E.LMVQVKKD...
Retrocopy VYVVNYPKDN*RRRDKTDASLAIKVKRAVQKTSDLVVLGLPWKTTEQDLKEYFSSFREILMVQVKKDVRS

Parental  GHSKGFGFVRFTEYETQVKV-MSQRHMIDGRWCDCKLPNSKQSADEPLRSRKVFVGRCTEDMTEDELRQF
          ..SKGFGF..F..YETQVK..MS..H..DG.WCDC.LPNSK....E.LRS...F.G.CTE.M..D.L..F
Retrocopy SYSKGFGFAHFIKYETQVKE<MS*QHKTDG*WCDCTLPNSKKTLNETLRSERIFMGYCTENMNSDKLH*F

Parental  FSQYGEVMDVFIPKPFRAFAFVT-FADDQIAQSLCGEDLIIKGISVHISNA-EPKHNSNRQLE
          F.Q..EV.DVFIPKP.RAFAFVT..AD...AQSL.GE.LIIKGI..HISNA...KHNSN.Q.E
Retrocopy FWQDREVVDVFIPKPLRAFAFVT<IAD**LAQSLSGENLIIKGIRIHISNA<RHKHNSNKQKE

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	33.19 RPM
SRP051959_heart	0.00 RPM	44.92 RPM
SRP051959_kidney	0.00 RPM	43.53 RPM
SRP051959_liver	0.00 RPM	32.49 RPM
SRP051959_lung	0.00 RPM	56.89 RPM
SRP051959_lymph_node	0.00 RPM	58.40 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.76 RPM
SRP051959_spleen	0.00 RPM	54.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2457 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2457 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3637
Pan troglodytes	retro_ptro_2460
Macaca mulatta	retro_mmul_1847

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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,