RetrogeneDB ID: retro_hsap_964

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:11665640..11667072(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000270863
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX55
• Ensembl ID: ENSG00000111364
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 [Source:HGNC Symbol;Acc:20085]

Sequence

>retro_hsap_964
TCTCCTCTGTTCCAAGTTTAAGAGTTTAAGCAACAAGGTGGGAACATCACTGTGGCCATTCCAGGCCACTTGAAGACAGG
TTCTGAAGGAAGGCAGAAGGCTTGTATCTGGCCAGCTGTGTGTGATCCCTGCATATCCTGGTGTTGGATGAGGCAGACAG
ACTTCTGGACATGGGATTTGAGGCAAGCATAAATACCATCCTGGAGTTTTTGCCAAAGCAGAGGAGAACAGGCCTTTTCT
CTGCCACTCAGAAGCAGGAAGTGGAGAACTTGGGGAGAGTGGGATGCCGGAACCCTGTCCAGTCTCAGTGAAGAAGGGTG
TGGCAGCCAGCAGTGCCCAGAACACCACTCTCCCCTGGAAAACTACTACATGGTATGCAAGGCAGATGAGAAATTTAATC
AGCTGCTACATTTTCTTCGCAGTCATAAGCAAGAGCAACACCTGGTCTTCTTTAGCACTTGCACCTGTGTGGAATACTAC
AGGAAGGCTCTGGAGGTGCTGATGAAGAGTGTGAAGATTGTGTGCATCCATGGAAAGATGAAATACGATCTTCATGCAAA
TTGAAAATTGCAATTGTTCTGCAAATTGCAAAGTGGAATTTTAGTGTGCACTGATGTGGTGGCCCAGGAATCAATGTTCC
TGAAGTAAACTGGGTTTTGCAGTACAATCGCCCCTACAATGCAAGTGCCTTTGTGCAGCACTGTAGCCGCACAGCCCTCA
TTGGCCACAGAGGCAGAGCTCTGGTGTTCCTCCTGCCCGTGGAAGAGTCATACATCAATTTCCTTGCAATTAACCAAAAA
TGCCCCCTGGCGGAGATGAAACTCTAGAAAAACACAGCTGACCTTCTGCCAAAACTCAAGTCCATGACCCTGGCAGAAAA
ATCTGTGTTTGAAAAGGGCATGAAAGCTTTTGTGTCCTATGTCCAGGCTTATGCAAAGTAAGAATGCAACCTGATTTTCA
GATTAAATAATCTTGATTTTGCAAGTCTTGCTCGAGGTTTTTCCCTGCTGAGAATGCCCAAGATGCCAGAATTGAGAGGA
AAGCAGTTTCCAGATTTTGTGCCTGTGGACATTAATACAGACACTATTTCATTTAAAGATAAAATTAGAGAAAAGCAGAG
GCAGAAATTACTGGAGCAACAAAGGAAAGAGAAAAACAGAAAATGAAGGGAGAAGAAAATTCATAAAAAATAAAGATTGG
TCGAAGCAGAAGGCCAAAAAAGAGAAGAAGAAAAACATGAATGAGATAAGGAAAAGGGAAGCATGTTCTGATACAAAGAT
GAGGACATGGAAGAACTTCTCAATGATTCAGAGCTCTTGAAAAAAATTTTTAAAGGCAAAATTACTGAAGAATTTGAGAA
GGACTTATTGACAAGTGGCAAAAGAACAATCAAGACAGCCAATTTAATGTCTCAGATTTGGAAGATGACTGC

Alignment

ORF - retro_hsap_964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 79.83 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NPGEDVERFKQQGGNIIVATPGRL-EDMFRRKAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILE
          .P...V..FKQQGGNI.VA.PG.L.ED.F.RKAEGL.LASCV.SL..LVLDEADRLLDMGFEASINTILE
Retrocopy SPLFQV*EFKQQGGNITVAIPGHL<EDRF*RKAEGLYLASCV*SLHILVLDEADRLLDMGFEASINTILE

Parental  FLPKQRRTGLFSATQTQEVENLVRAGLRNPVR-VSVKEKGVAASSAQKTP-SRLENYYMVCKADEKFNQL
          FLPKQRRTGLFSATQ.QEVENL.R.G.RNPV..VSVK.KGVAASSAQ.T..S.LENYYMVCKADEKFNQL
Retrocopy FLPKQRRTGLFSATQKQEVENLGRVGCRNPVQ<VSVK-KGVAASSAQNTT<SPLENYYMVCKADEKFNQL

Parental  VHFLRNHKQEKHLVFFSTCACVEYYGKALEVLVKGVKIMCIHG--KMKYKRNKIFMEFRKLQSGILVCTD
          .HFLR.HKQE.HLVFFSTC.CVEYY.KALEVL.K.VKI.CIHG..K.....N.....F.KLQSGILVCTD
Retrocopy LHFLRSHKQEQHLVFFSTCTCVEYYRKALEVLMKSVKIVCIHGKMKYDLHAN*KLQLFCKLQSGILVCTD

Parental  VMAR-GIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFLLPMEESYINFLAINQKCPLQEMK
          V.A..GI..PEVNWVLQY..P.NASAFV..C.RTA.IGH.G.ALVFLLP.EESYINFLAINQKCPL.EMK
Retrocopy VVAQ<GINVPEVNWVLQYNRPYNASAFVQHCSRTALIGHRGRALVFLLPVEESYINFLAINQKCPLAEMK

Parental  PQRNTADLLPKLKSMALADRAVFEKGMKAFVSYVQAYAKHECNLIFRLKDLDFASLARGFALLRMPKMPE
          ...NTADLLPKLKSM.LA...VFEKGMKAFVSYVQAYAK.ECNLIFRL..LDFASLARGF.LLRMPKMPE
Retrocopy L*KNTADLLPKLKSMTLAEKSVFEKGMKAFVSYVQAYAK*ECNLIFRLNNLDFASLARGFSLLRMPKMPE

Parental  LRGKQFPDFVPVDVNTDTIPFKDKIREKQRQKLLEQQRRE-KTENEGRRKFIKNKAWSKQKAKKEKKKKM
          LRGKQFPDFVPVD.NTDTI.FKDKIREKQRQKLLEQQR.E.KTENEGRRKF..................M
Retrocopy LRGKQFPDFVPVDINTDTISFKDKIREKQRQKLLEQQRKE>KTENEGRRKFXXXXXXXXXXXXXXXXXXM

Parental  NEKRKREEGSD-IEDEDMEELLNDTRLLKKLKKGKITEEEFEKGLLTTGKRTIKTVDL-GISDLEDDC
          NE.RKRE..SD...DEDMEELLND..LLKK..KGKIT.EEFEK.LLT.GKRTIKT..L...SDLEDDC
Retrocopy NEIRKREACSD<YKDEDMEELLNDSELLKKIFKGKIT-EEFEKDLLTSGKRTIKTANL<NVSDLEDDC

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	0.26 RPM	12.40 RPM
bodymap2_adrenal	0.08 RPM	25.10 RPM
bodymap2_brain	0.19 RPM	13.01 RPM
bodymap2_breast	0.00 RPM	13.83 RPM
bodymap2_colon	0.00 RPM	12.16 RPM
bodymap2_heart	0.02 RPM	3.27 RPM
bodymap2_kidney	0.12 RPM	13.50 RPM
bodymap2_liver	0.04 RPM	7.94 RPM
bodymap2_lung	0.09 RPM	7.68 RPM
bodymap2_lymph_node	0.15 RPM	27.15 RPM
bodymap2_ovary	0.21 RPM	22.86 RPM
bodymap2_prostate	0.00 RPM	17.98 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.15 RPM
bodymap2_testis	0.02 RPM	17.02 RPM
bodymap2_thyroid	0.15 RPM	21.20 RPM
bodymap2_white_blood_cells	0.00 RPM	13.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_964 was not detected

EST

No EST(s) were mapped for retro_hsap_964 retrocopy.

TSS

No TSS is located nearby retro_hsap_964 retrocopy 5' end.

Lab

retro_hsap_964 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_964 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_668

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000111364	1 retrocopy	retro_hsap_964 ,
Gorilla gorilla	ENSGGOG00000026102	1 retrocopy	retro_ggor_776,
Pan troglodytes	ENSPTRG00000005601	1 retrocopy	retro_ptro_668,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.19 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.27 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.20 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).