RetrogeneDB ID: retro_hsap_3660

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:131505467..131506418(-)
• Located in intron of: ENSG00000118507

Retrocopy information

• Ensembl ID: ENSG00000218857
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DPF2
• Ensembl ID: ENSG00000133884
• Aliases: DPF2, REQ, UBID4, ubi-d4
• Description: D4, zinc and double PHD fingers family 2 [Source:HGNC Symbol;Acc:9964]

Sequence

>retro_hsap_3660
TACTCGTACCCTGCCCAGCACTGGCGGAAAAAGCGGTGAGCCCACCCCTGTGAAGATCCACAATTTTTCTTCCCACCTAT
TAAGCCAGACACAGACCCCACCCTGAAGAAGGAGGGGCTGATCTCTCAGGACAGCAGCAGTTTAGAGGTTCTGTTGCACA
CTGACCCCCTGGGGAAGCGAGGTACCCCAGATCCCCGAGTTGATGATGACAGCCTGGGCAAGTTTCCTGTGACAAACAGT
CAAGCACGAAAGCGGATCCTAGAACCAGATGACTTCCTGGATGACCTCGATGATGAGTACTGTGAAGATGCTCCCAAGCA
TCGGGGAAAGGGGTAATCCAAGGGTAAAGGTGTGGCAGTGCCCATAAGGAGCTGGATGCTTCCAACCTGGAGGACCAGGA
TAAGCCCTATGCCTGTGACATTTGTGGAAAACGTTACAAGAACCGACCAGGCCTCAGTTACCACTATGCCCACTCTCACT
TGGCTGAGGAGGGCGAGGACAAAGAAGACTCCCAACCACCCACTCCTGTTTCCCAGAGGTCTGAGGAACAGAAATCCAAA
AAGGGTCCTGATGGATTTGCCTTGCCCAACAACTACTGTAACTTCTGCCTGGGGAACTCAAAGATTAACAAGAAGATGGG
ACAACCTGAGGAGGTGGTGTCCTGTTTCGACTGTGGCTGCTCAGGGCATCCATCTTGCCTCCATTTCACCCCCATGATGA
TGGGGCAGTGAAGACATACTGCTGGCAATGCATCGAGCACAAATGTTGCGATATCTGCGGCACCTCTGAAGATGATGACC
AGCTGGGCTTTTGTGATGCTGCGATCATGGCTACGAAATGTACTGTCTCACTCCGTCCATATCTGAGCCCCCTGAAGGAA
GTTGGAGGTGCCACCTGTGTCTGGACCTGTTGAAGGAGAAAGCTTCCATCTACCAGAACAAGAACTCCTCT

Alignment

ORF - retro_hsap_3660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 81.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YSYPARRWRKKRRAHPPEDPRLSFPSIKPDTDQTLKKEGLISQDGSSLEALLRTDPLEKRGAPDPRVDDD
          YSYPA..WRKKR.AHP.EDP...FP.IKPDTD.TLKKEGLISQD.SSLE.LL.TDPL.KRG.PDPRVDDD
Retrocopy YSYPAQHWRKKR*AHPCEDPQFFFPPIKPDTDPTLKKEGLISQDSSSLEVLLHTDPLGKRGTPDPRVDDD

Parental  SLGEFPVTNSRARKRILEPDDFLDDLDDEDYEEDTPKRRGKGKSKGKGV-GSARKKLDASILEDRDKPYA
          SLG.FPVTNS.ARKRILEPDDFLDDLDDE.Y.ED.PK.RGKG.SKGKGV.GSA.K.LDAS.LED.DKPYA
Retrocopy SLGKFPVTNSQARKRILEPDDFLDDLDDE-YCEDAPKHRGKG*SKGKGV<GSAHKELDASNLEDQDKPYA

Parental  CDICGKRYKNRPGLSYHYAHSHLAEEEGEDKEDSQPPTPVSQRSEEQKSKKGPDGLALPNNYCDFCLGDS
          CDICGKRYKNRPGLSYHYAHSHLA.EEGEDKEDSQPPTPVSQRSEEQKSKKGPDG.ALPNNYC.FCLG.S
Retrocopy CDICGKRYKNRPGLSYHYAHSHLA-EEGEDKEDSQPPTPVSQRSEEQKSKKGPDGFALPNNYCNFCLGNS

Parental  KINKKTGQPEELVSCSDCGRSGHPSCLQFTPVMM-AAVKTYRWQCIECKCCNICGTSENDDQLLFCDD-C
          KINKK.GQPEE.VSC.DCG.SGHPSCL.FTP.MM..AVKTY.WQCIE.KCC.ICGTSE.DDQL.FCD..C
Retrocopy KINKKMGQPEEVVSCFDCGCSGHPSCLHFTPMMM<GAVKTYCWQCIEHKCCDICGTSEDDDQLGFCDA<C

Parental  DRGYHMYCLTPSMSEPPEGSWSCHLCLDLLKEKASIYQNQNSS
          D.GY.MYCLTPS.SEPPEGSW.CHLCLDLLKEKASIYQN.NSS
Retrocopy DHGYEMYCLTPSISEPPEGSWRCHLCLDLLKEKASIYQNKNSS

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	31.49 RPM
bodymap2_adrenal	0.06 RPM	40.92 RPM
bodymap2_brain	0.05 RPM	31.53 RPM
bodymap2_breast	0.00 RPM	28.46 RPM
bodymap2_colon	0.00 RPM	37.99 RPM
bodymap2_heart	0.09 RPM	25.16 RPM
bodymap2_kidney	0.08 RPM	27.55 RPM
bodymap2_liver	0.02 RPM	12.57 RPM
bodymap2_lung	0.00 RPM	36.01 RPM
bodymap2_lymph_node	0.00 RPM	56.26 RPM
bodymap2_ovary	0.04 RPM	66.85 RPM
bodymap2_prostate	0.12 RPM	67.93 RPM
bodymap2_skeletal_muscle	0.00 RPM	39.80 RPM
bodymap2_testis	0.08 RPM	70.89 RPM
bodymap2_thyroid	0.04 RPM	41.58 RPM
bodymap2_white_blood_cells	0.00 RPM	67.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3660 was not detected

EST

No EST(s) were mapped for retro_hsap_3660 retrocopy.

TSS

No TSS is located nearby retro_hsap_3660 retrocopy 5' end.

Lab

retro_hsap_3660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023858	1 retrocopy	retro_fcat_1341,
Homo sapiens	ENSG00000133884	1 retrocopy	retro_hsap_3660 ,
Macaca mulatta	ENSMMUG00000012317	1 retrocopy	retro_mmul_1794,
Nomascus leucogenys	ENSNLEG00000005574	1 retrocopy	retro_nleu_516,
Tarsius syrichta	ENSTSYG00000000038	1 retrocopy	retro_tsyr_1932,

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	0.04 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	0.00 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	0.06 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	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 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	0.02 RPM

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Indel association:

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