RetrogeneDB ID: retro_hsap_4153

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:35449888..35450351(+)
• Located in intron of: ENSG00000179766

Retrocopy information

• Ensembl ID: ENSG00000244213
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSG00000086666
• Aliases: ZFAND6, AWP1, ZA20D3, ZFAND5B
• Description: zinc finger, AN1-type domain 6 [Source:HGNC Symbol;Acc:30164]

Sequence

>retro_hsap_4153
AGCCAACCTGCAACCTCTGAATCTTTACCAGTTCAATGCACAGATGGCAGTGTCCCAGAAGCCCAGTCAACATTAGACTC
TACATCTTCATCTATGCAGCCAAGCCCTGTATCAAATCAGTCACTTTTATCAGAATCTGTAGCATCTTCTCAATTGGACA
GTACATCTGTGGACAAGCAGTACCTGAAACAGAAGATCTGCAGGCTTCAGTATCAGACATGGCACAGCAGCCATCTGAAG
AGCAAAGCAAGTCTCTTGAAAAACCAAAACAAAAAAAGAATCTCTGTTTCATGTGCAGGAAGAAAGTGGGACTTACTAGG
TTTGAATGCGGTGTAGAAATGTTTACTGTGGTGTACACTGTTACTCAGATCTACACAATTGCTCTTAAAATTACAAAGCT
GATGCCGCTGAGAAAATCAGAAAAGAAAATCCAGTAGTTGTTGGCGAGAAGATCCAAAAGATT

Alignment

ORF - retro_hsap_4153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 74.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVSSLSESLPVQCTDGSVPEAQSALDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK-AVPETEDVQA
          S....SESLPVQCTDGSVPEAQS.LDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK.AVPETED.QA
Retrocopy SQPATSESLPVQCTDGSVPEAQSTLDSTSSSMQPSPVSNQSLLSESVASSQLDSTSVDK<AVPETEDLQA

Parental  SVSDTAQQPSEEQSKSLEKPKQKKNRCFMCRKKVGLTGFEC-RCGNVYCGVHRYSDVHNCSYNYKADAAE
          SVSD.AQQPSEEQSKSL.......N.CFMCRKKVGLT.FEC.RC.NVYCGVH.YSD.HNCS.NYKADAAE
Retrocopy SVSDMAQQPSEEQSKSLXXXXXXXNLCFMCRKKVGLTRFEC<RCRNVYCGVHCYSDLHNCS*NYKADAAE

Parental  KIRKENPVVVGEKIQKI
          KIRKENPVVVGEKIQKI
Retrocopy KIRKENPVVVGEKIQKI

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	65.20 RPM
bodymap2_adrenal	0.04 RPM	77.42 RPM
bodymap2_brain	0.00 RPM	37.97 RPM
bodymap2_breast	0.14 RPM	92.24 RPM
bodymap2_colon	0.00 RPM	72.18 RPM
bodymap2_heart	0.00 RPM	47.19 RPM
bodymap2_kidney	0.00 RPM	73.02 RPM
bodymap2_liver	0.00 RPM	46.22 RPM
bodymap2_lung	0.00 RPM	71.64 RPM
bodymap2_lymph_node	0.00 RPM	68.91 RPM
bodymap2_ovary	0.00 RPM	61.49 RPM
bodymap2_prostate	0.00 RPM	62.21 RPM
bodymap2_skeletal_muscle	0.00 RPM	67.42 RPM
bodymap2_testis	0.92 RPM	155.54 RPM
bodymap2_thyroid	0.04 RPM	113.29 RPM
bodymap2_white_blood_cells	0.00 RPM	79.24 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4153 was not detected

EST

No EST(s) were mapped for retro_hsap_4153 retrocopy.

TSS

No TSS is located nearby retro_hsap_4153 retrocopy 5' end.

Lab

retro_hsap_4153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4153 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2824
Gorilla gorilla	retro_ggor_2790

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153 ,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

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