RetrogeneDB ID: retro_hsap_2273

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:65727849..65728466(-)
• Located in intron of: ENSG00000204929

Retrocopy information

• Ensembl ID: ENSG00000237979
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJB12
• Ensembl ID: ENSG00000148719
• Aliases: DNAJB12, DJ10
• Description: DnaJ (Hsp40) homolog, subfamily B, member 12 [Source:HGNC Symbol;Acc:14891]

Sequence

>retro_hsap_2273
AAGCAGTATGACCACTTGGGCGATAACAGGAGTCAGGCAGTCAGGTCCAGCATCGTCATGGGGATTTCCACCACGGCTTT
GAGGCTGACATCTCCCCTGAAGACCTCTTCAACATGTTCTTTGGCAATGGCTTCCCTTCTAGTAAAGTCTACGTCTACAG
CAATGGCTGCATGCGCTATACCTACCAGCAAAGGCAGGGCTGCAGGGAGAAGCGGAGTGACGGCAGCTTGCGGGTGTTCG
TGCAGCTGATACCCATCCTCATCCTCATGTCAGCTCTCAGCCAGCTCATGGTCTCCAGTCCACCCTACAGTCTGAGCCCA
AGACTGTTTGTGGGCCACATCACAGGCGAGTCACTGACCACCTGAGTGTCATCTACTATGTGGCAGGCATTTTCTCCGAG
GAGTACACAGGCTCCAGCCTCCAAACAGTCAAACCGAATGTGAAAGATGATTATATCGCCAACCTCTGGAACAACTGCTG
GACGGAGAAGCAGCAGATGAAAGGCTTGCTGTACCGAGGCCGCTACTTTGGTGACACAGATATGTACCACAAAGCACAGA
AGATGGGCAGCCCCCTGCTGCAGCCAGCTGTCACAGGATCAGGCCTCCCTGCATGGA

Alignment

ORF - retro_hsap_2273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.3 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KQYDQFGDDKSQAARHG-HGHGDFHRGFEADISPEDLFNMFFGGGFPSSNVHVYSNGRMRYTYQQRQDRR
          KQYD..GD..SQA.R...H.HGDFH.GFEADISPEDLFNMFFG.GFPSS.V.VYSNG.MRYTYQQRQ..R
Retrocopy KQYDHLGDNRSQAVRSS<HRHGDFHHGFEADISPEDLFNMFFGNGFPSSKVYVYSNGCMRYTYQQRQGCR

Parental  DNQGDGGLGVFVQLMPILILILVSALSQLMVSSPPYSLSPRPSVGHI-HRRVTDHLGVVYYVGDTFSEEY
          ....DG.L.VFVQL.PILIL...SALSQLMVSSPPYSLSPR..VGHI.HRRVTDHL.V.YYV...FSEEY
Retrocopy EKRSDGSLRVFVQLIPILILM--SALSQLMVSSPPYSLSPRLFVGHI<HRRVTDHLSVIYYVAGIFSEEY

Parental  TGSSLKTVERNVEDDYIANLRNNCWKEKQQKEGLLYRARYFGDTDMYHRAQKMGT-PSCSRLSEVQASLH
          TGSSL.TV..NV.DDYIANL.NNCW.EKQQ..GLLYR.RYFGDTDMYH.AQKMG..P.CS.LS..QASLH
Retrocopy TGSSLQTVKPNVKDDYIANLWNNCWTEKQQMKGLLYRGRYFGDTDMYHKAQKMGS>PCCSQLSQDQASLH

Parental  G
          G
Retrocopy G

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	0.08 RPM	40.27 RPM
bodymap2_adrenal	0.00 RPM	41.10 RPM
bodymap2_brain	0.05 RPM	18.19 RPM
bodymap2_breast	0.04 RPM	36.30 RPM
bodymap2_colon	0.00 RPM	22.12 RPM
bodymap2_heart	0.04 RPM	23.89 RPM
bodymap2_kidney	0.14 RPM	35.41 RPM
bodymap2_liver	0.02 RPM	28.33 RPM
bodymap2_lung	0.04 RPM	24.65 RPM
bodymap2_lymph_node	0.00 RPM	26.48 RPM
bodymap2_ovary	0.00 RPM	32.17 RPM
bodymap2_prostate	0.12 RPM	34.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	48.56 RPM
bodymap2_testis	0.02 RPM	40.89 RPM
bodymap2_thyroid	0.02 RPM	42.71 RPM
bodymap2_white_blood_cells	0.00 RPM	43.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2273 was not detected

EST

No EST(s) were mapped for retro_hsap_2273 retrocopy.

TSS

No TSS is located nearby retro_hsap_2273 retrocopy 5' end.

Lab

retro_hsap_2273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2273 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1608
Gorilla gorilla	retro_ggor_1691
Pongo abelii	retro_pabe_1945
Callithrix jacchus	retro_cjac_1200

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007303	1 retrocopy	retro_cjac_1200,
Dasypus novemcinctus	ENSDNOG00000009977	1 retrocopy	retro_dnov_866,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273 ,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Gorilla gorilla	ENSGGOG00000000683	1 retrocopy	retro_ggor_1691,
Macropus eugenii	ENSMEUG00000002024	2 retrocopies	retro_meug_1115, retro_meug_1511,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 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	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 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	0.05 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 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	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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