RetrogeneDB ID: retro_hsap_322

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:235778691..235779696(+)
• Located in intron of: ENSG00000168243

Retrocopy information

• Ensembl ID: ENSG00000227236
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC39A14
• Ensembl ID: ENSG00000104635
• Aliases: SLC39A14, LZT-Hs4, NET34, ZIP14, cig19
• Description: solute carrier family 39 (zinc transporter), member 14 [Source:HGNC Symbol;Acc:20858]

Sequence

>retro_hsap_322
AGTGCAACTGAAGTGTGGGGATACGATCTCCTCTATGTGACTGTCATCTCCCTCTGCTCCCTCATGGGCACCATCGTGGT
GCCTTCAAGAAGGCCTTTTACAGAAGGAAGCTGCTGCTCCACGTCATAGCTCTGGCGATTGGAATCCTCTAGTCCAATGT
GCTCTCCTAGCTCATTCCTGGGGCTTTTGATTTCAACCCTCTGGAAGATGATTATGTGTCCAAGTCTGCAGTGGTGTCTG
GGGGCTTTTATTTTTATTTTTCAGAGATCTTGAAGATGTTTCTCAAACAGGAAAATGAACATCACATAGACATAGCCATT
ATGCCTCTGAGAGGCTTCCTTCCAAGAAGCACCAGGAGGAGGGGGGTGATGGAGAAGCTGCAGAATGGGGACCTGGACCA
CATGAGCCCTCAGCACTGCCACAGTGAACTGGATGGCAAGCAGTCCATGATGGATGGGAAGGTCGTGGTGGGCTCACTCT
CTGTGCTGGTTCTGCAGGCTCCCCAGAGTGCCTGCTGGAGCTGAAAGGTGTCCACTACTTTATCAGCACTCTGGCCTGGG
TGATCACCCTAAGCAACAGCCTCCACAATGTCCTCAGCAGCCTGGCCACTGGCGCCTCTTTCACCGTCTGTGTGGTCCAA
GGCCTCGGCACCTGGTGGCCGTCTTCCATGAGGAGTTCCCACATGACTTTGTCATCCTGCTTAGCGCTAGGAGGACCATT
CAGCACTGTCTTCTTCAACCCCCTTCCGCCTGCTGCTATGTGGGTCTGGCCTTTGGCATCCTGGCCAGCAGCCACTTCTC
TGCCAACTGAATTTTTGTGCTGGTTGGAGGAATGTTCTTGAATATTGCTGTGGTTGATATGTTCCCTGAGACGAATGAGG
TCTGCCAAGAGGATGGGAGGAAGGGCAGCATCTCCATCCCCTTTGTCATTCAGAACCTGGGTCTGTTGGCCAGATTCACC
GTCATGCTGGTCCTCGTGATATATTCAGGACAGATCCAGATTGGG

Alignment

ORF - retro_hsap_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.34 %
• Parental protein coverage: 69.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SAVEVWGYGLLCVTVISLCSLLGASVVP-FMKKTFYKRLLLYFIALAIGTLYSNALFQLIPEAFGFNPLE
          SA.EVWGY.LL.VTVISLCSL.G..VVP.F.K......LLL..IALAIG.L.SN.L..LIP.AF.FNPLE
Retrocopy SATEVWGYDLLYVTVISLCSLMGTIVVP<FKKAFYRRKLLLHVIALAIGIL*SNVLS*LIPGAFDFNPLE

Parental  DYYVSKSAVVFGGFYLFFFTEKILKILLKQKNEHH-HGHSHYASESLPSKKDQEE-GVMEKLQNGDLDHM
          D.YVSKSAVV.GGFY..F....ILK..LKQ.NEHH.H.HSHYASE.LPSKK.QEE.GVMEKLQNGDLDHM
Retrocopy DDYVSKSAVVSGGFYFYF--SEILKMFLKQENEHH<HRHSHYASERLPSKKHQEE>GVMEKLQNGDLDHM

Parental  IPQHCSSELDGKAPMVDEKVIVGSLSVQDLQASQSACY-WLKGVRYSDIGTLAWMITLSDGLHNFIDGLA
          .PQHC.SELDGK..M.D.KV.VGSLSV..LQA.QSAC...LKGV.Y..I.TLAW.ITLS..LHN....LA
Retrocopy SPQHCHSELDGKQSMMDGKVVVGSLSVLVLQAPQSACW<ELKGVHYF-ISTLAWVITLSNSLHNVLSSLA

Parental  IGASFTVSVFQGIST-SVAILCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGILAGSHF
          .GASFTV.V.QG..T..VA...EEFPH...DFVILL.A...IQ..L.....SAC.CY.GLAFGILA.SHF
Retrocopy TGASFTVCVVQGLGT<LVAVFHEEFPH---DFVILLSARRTIQHCL-LQPPSAC-CYVGLAFGILASSHF

Parental  SANWIFALAGGMFLYISLADMFPEMNEVCQEDERKGSILIPFIIQNLGLLTGFTIMVVLTMYSGQIQIG
          SAN.IF.L.GGMFL.I...DMFPE.NEVCQED.RKGSI.IPF.IQNLGLL..FT.M.VL..YSGQIQIG
Retrocopy SAN*IFVLVGGMFLNIAVVDMFPETNEVCQEDGRKGSISIPFVIQNLGLLARFTVMLVLVIYSGQIQIG

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	120.64 RPM
bodymap2_adrenal	0.00 RPM	80.71 RPM
bodymap2_brain	0.00 RPM	58.20 RPM
bodymap2_breast	0.00 RPM	30.33 RPM
bodymap2_colon	0.00 RPM	195.66 RPM
bodymap2_heart	0.00 RPM	192.05 RPM
bodymap2_kidney	0.00 RPM	241.69 RPM
bodymap2_liver	0.00 RPM	957.14 RPM
bodymap2_lung	0.00 RPM	141.05 RPM
bodymap2_lymph_node	0.00 RPM	218.79 RPM
bodymap2_ovary	0.06 RPM	126.15 RPM
bodymap2_prostate	0.00 RPM	114.78 RPM
bodymap2_skeletal_muscle	0.00 RPM	68.37 RPM
bodymap2_testis	0.00 RPM	111.37 RPM
bodymap2_thyroid	0.00 RPM	100.73 RPM
bodymap2_white_blood_cells	0.00 RPM	12.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_322 was not detected

EST

No EST(s) were mapped for retro_hsap_322 retrocopy.

TSS

No TSS is located nearby retro_hsap_322 retrocopy 5' end.

Lab

retro_hsap_322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_322 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_348

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018834	1 retrocopy	retro_dnov_1567,
Homo sapiens	ENSG00000104635	1 retrocopy	retro_hsap_322 ,
Gorilla gorilla	ENSGGOG00000003765	1 retrocopy	retro_ggor_348,
Nomascus leucogenys	ENSNLEG00000015557	1 retrocopy	retro_nleu_1765,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 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	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 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	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 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).