RetrogeneDB ID: retro_hsap_2168

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:153246389..153247146(+)
• Located in intron of: ENSG00000157827

Retrocopy information

• Ensembl ID: ENSG00000213197
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSG00000090273
• Aliases: NUDC, HNUDC, MNUDC, NPD011
• Description: nuclear distribution C homolog (A. nidulans) [Source:HGNC Symbol;Acc:8045]

Sequence

>retro_hsap_2168
AGAAGGCCCGGTGGGAGAAGAGAACCCGGGAGAAGGTGGAGCGGGTGGCCGGGCTGGCCAAGGAAGCCAAGTCAGAGACC
TCGGGGCCCCAGATAAAGGCAGACAGGCAGAGAGGCTGCAGCTAGAGATTGACCAGAAAAAGGATGCAGAGAATCATGAG
GCCCAGCTCAAGAACGGCAGCCTTGACTCCCCAGGAAAGCAGGAGAAGAAGGAGGAAGATGAGGAGGACAAAGGAAAACT
GAAGCCCAACCTAGGCAACGGGGCAGACCTGCCCAATTACTGCTGGACCCAGAGCCTGTCGGAGCTGGACCTGGTGGTCC
CTTTCCGTGTAAACTTCCGGCTGAAAGGGAAGGACATGGTGGTGGACATCCAGGGGCAGCACCTCCGGGTGGGGCTCAAG
GGGCAGCCAGCAATCATCGATGGGGAGCTCTACAACGAAGTGAAGGTAGGGGAGAGCTCGTGGCTCATTGAGGATGGCAA
GGTGGTGACTGTGCATCTTGAGAAGATCAATAAGATGGAGTGGTGGAGCTGCTTGGTGTCCAGTGACCCTAAGATCAATA
CCAAGATGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAATGAGACTCGCAGCATGGTGGAAAAGATGATGTAT
GACCAGAGACAGAAGTCCATGGGGCTGCCAATCTCAGACGAACAGAAGAAACAGGAGATTCTGAAGAAGTTCATGGATCA
GCATCTGGAGATGGATTTTTCCAAGGCCAAATTCAAC

Alignment

ORF - retro_hsap_2168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 77.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQEAERREKA-ERAARLAKEAKSETSGPQIKELTDE-EAERLQLEIDQKKDAENHEAQLKNGSLDSPGKQ
          R....RRE...E...R.A..AK...S............AERLQLEIDQKKDAENHEAQLKNGSLDSPGKQ
Retrocopy RRPGGRREPG<EKVERVAGLAKEAKSETSGPQIKAD<QAERLQLEIDQKKDAENHEAQLKNGSLDSPGKQ

Parental  DTEEDEEEDEKDKGKLKPNLGNGADLPNYRWTQTLSELDLAVPFCVNFRLKGKDMVVDIQRRHLRVGLKG
          ...E..EEDE.DKGKLKPNLGNGADLPNY.WTQ.LSELDL.VPF.VNFRLKGKDMVVDIQ..HLRVGLKG
Retrocopy ---EKKEEDEEDKGKLKPNLGNGADLPNYCWTQSLSELDLVVPFRVNFRLKGKDMVVDIQGQHLRVGLKG

Parental  QPAIIDGELYNEVKVEESSWLIEDGKVVTVHLEKINKMEWWSRLVSSDPEINTKKINPENSKLSDLDSET
          QPAIIDGELYNEVKV.ESSWLIEDGKVVTVHLEKINKMEWWS.LVSSDP.INTK.INPENSKLSDLD.ET
Retrocopy QPAIIDGELYNEVKVGESSWLIEDGKVVTVHLEKINKMEWWSCLVSSDPKINTKMINPENSKLSDLDNET

Parental  RSMVEKMMYDQRQKSMGLPTSDEQKKQEILKKFMDQHPEMDFSKAKFN
          RSMVEKMMYDQRQKSMGLP.SDEQKKQEILKKFMDQH.EMDFSKAKFN
Retrocopy RSMVEKMMYDQRQKSMGLPISDEQKKQEILKKFMDQHLEMDFSKAKFN

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	0.02 RPM	79.19 RPM
bodymap2_adrenal	0.06 RPM	81.73 RPM
bodymap2_brain	0.47 RPM	107.61 RPM
bodymap2_breast	0.16 RPM	62.74 RPM
bodymap2_colon	0.14 RPM	146.22 RPM
bodymap2_heart	0.07 RPM	44.51 RPM
bodymap2_kidney	0.15 RPM	66.84 RPM
bodymap2_liver	0.00 RPM	73.93 RPM
bodymap2_lung	0.09 RPM	74.03 RPM
bodymap2_lymph_node	0.22 RPM	60.21 RPM
bodymap2_ovary	0.02 RPM	111.90 RPM
bodymap2_prostate	0.23 RPM	97.93 RPM
bodymap2_skeletal_muscle	0.00 RPM	84.30 RPM
bodymap2_testis	0.04 RPM	132.56 RPM
bodymap2_thyroid	0.26 RPM	105.49 RPM
bodymap2_white_blood_cells	0.00 RPM	37.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2168 was not detected

EST

No EST(s) were mapped for retro_hsap_2168 retrocopy.

TSS

No TSS is located nearby retro_hsap_2168 retrocopy 5' end.

Lab

retro_hsap_2168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2168 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1655
Gorilla gorilla	retro_ggor_1720
Pongo abelii	retro_pabe_2055

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168 , retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 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	0.05 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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