RetrogeneDB ID: retro_hsap_1209

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:60848912..60849717(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000238213
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSG00000120948
• Aliases: None
• Description: TAR DNA binding protein [Source:HGNC Symbol;Acc:11571]

Sequence

>retro_hsap_1209
ATATCTGAATATATTCGCGTACCGAAGATGAGAAGGATGAGCCCATTGAAATACCATCGGAAGACGATGGGACGGTGCTG
CTGTCCATGGTTACAGCCCAGTTTCCAGGGGTGTGTGGGCTTCGCTACAGAAATCCAGTGTCTCAGTGTATGAGAGGTGT
CCGGTTGGTAGAAGGAATTCTTCATGCCCCCGATGCTGGCTGGGAAATCTGGTGTATGTTGTCAACTATCCTAAAGATAA
CAAAAGAGAAATGGATGAGATAGATGCTTCATCAGCTGTGAAAGTGAAAAGAGCAGTCCAGAAAACATCTGATTTAGTAG
TGTTGGGTCGCACATGGAAAACAACTGAGCAGGACCTGAAAGAATATTTAAGTACCTTTGGAGATGTTCTTATGGTGCAG
GTCAAGAAAGATACTAACACTGGTCATTCAAAGAGGTTTGGCTTCGTTTGTTTTACGGAAGATGAAACACAGGTGAAAGT
AATGTCACAGCTACATATGATAGATGGACGATGGTGTGACTGTAAACTTCCCAATTCTAAGCAAAGCCCAGATAAGCCTT
TGAGAAGCATGAAAGTGGGGCGCTGAACAGAGGACATGATTGCAGATGAGCTGCGGCAGTTCTTCTGTCAGTACGGGGAA
GTGGTGGATGTCGTCATCCTCAAGCCATTCAGGACGTTTGCCTTTGTTACATTTGCAGATGATCAGGTTGCACAGTCTTT
TTGTGGAGAGGACTTGATCATTAAAGGAATCAGCATTCATATATCCAATGCCGAACCTAAGCACAACAGCAATAGACAGA
AAGAA

Alignment

ORF - retro_hsap_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEYIRV-TEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGW-
          .SEYIRV.TEDE.DEPIEIPSEDDGTVLLS.VTAQFPG.CGLRYRNPVSQCMRGVRLVEGILHAPDAGW.
Retrocopy ISEYIRV<TEDEKDEPIEIPSEDDGTVLLSMVTAQFPGVCGLRYRNPVSQCMRGVRLVEGILHAPDAGW<

Parental  GNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD
          GNLVYVVNYPKDNKR.MDE.DASSAVKVKRAVQKTSDL.VLG..WKTTEQDLKEY.STFG.VLMVQVKKD
Retrocopy GNLVYVVNYPKDNKREMDEIDASSAVKVKRAVQKTSDLVVLGRTWKTTEQDLKEYLSTFGDVLMVQVKKD

Parental  LKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELR
          ..TGHSK.FGFV.FTE.ETQVKVMSQ.HMIDGRWCDCKLPNSKQS.D.PLRS.K..VGR.TEDM..DELR
Retrocopy TNTGHSKRFGFVCFTEDETQVKVMSQLHMIDGRWCDCKLPNSKQSPDKPLRSMK--VGR*TEDMIADELR

Parental  EFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLE
          .FF.QYG.V.DV.I.KPFR.FAFVTFADDQ.AQS.CGEDLIIKGIS.HISNAEPKHNSNRQ.E
Retrocopy QFFCQYGEVVDVVILKPFRTFAFVTFADDQVAQSFCGEDLIIKGISIHISNAEPKHNSNRQKE

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
bodymap2_adipose	0.00 RPM	140.44 RPM
bodymap2_adrenal	0.08 RPM	161.67 RPM
bodymap2_brain	0.00 RPM	115.58 RPM
bodymap2_breast	0.08 RPM	131.36 RPM
bodymap2_colon	0.00 RPM	207.13 RPM
bodymap2_heart	0.00 RPM	83.30 RPM
bodymap2_kidney	0.00 RPM	141.14 RPM
bodymap2_liver	0.00 RPM	73.13 RPM
bodymap2_lung	0.05 RPM	153.29 RPM
bodymap2_lymph_node	0.00 RPM	173.87 RPM
bodymap2_ovary	0.00 RPM	279.34 RPM
bodymap2_prostate	0.00 RPM	144.52 RPM
bodymap2_skeletal_muscle	0.00 RPM	85.23 RPM
bodymap2_testis	0.00 RPM	172.17 RPM
bodymap2_thyroid	0.04 RPM	368.55 RPM
bodymap2_white_blood_cells	0.00 RPM	125.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1209 was not detected

EST

No EST(s) were mapped for retro_hsap_1209 retrocopy.

TSS

No TSS is located nearby retro_hsap_1209 retrocopy 5' end.

Lab

retro_hsap_1209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1209 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_828
Pongo abelii	retro_pabe_1008

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.19 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.31 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.34 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).