RetrogeneDB ID: retro_hsap_2471

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:32833761..32834334(-)
• Located in intron of: ENSG00000250917

Retrocopy information

• Ensembl ID: ENSG00000236456
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSG00000139726
• Aliases: DENR, DRP, DRP1, SMAP-3
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_hsap_2471
TCTGAATCCAGTGGGGCTGATTGCAAAGGAGACCCAAGGAACAGTGCCAAGTTAGATGCCAATTACCCACTTCGAGTCCT
TTATTGTGGAGTCTGTTCATTACCAACAGAGTACTGTGAATATATGCCTGATGTTGCTCATTGTAAACAATGGTTAGAGA
AGAATTTTCTAAATGAACTTGCAAAATTTACTGTAGAAAATTCACCCAAACAAGAAGCTGGAATTAGTGAGGGTCAAGGA
ACAGCAGGGGAAGAAGAGGAGAAGAAAAAACAGAAGAGAGGTGGAAGAGGCCAAATAAAACAAAAAAAGAAGACCATACC
ACAAAAGCTTACTAAGGCCAAAATTCCTAGAGCAAAGAAGAAACATGTGACAAGAGTGTGTGGCCTTGCAACTTTTGAAA
TTGATCTTAAAGAAGCACAAAGATTTTTGCTCAAAAATTCTCCTGTGCTGCCTCAGTAATGGGGAGGATGAAATTATTCG
GGGAGACTTTACAGATGACATAATTCATGTCATTCAGAAAAATGGCCAGAAGTAGATGATGACAGCATCAAAGATCTTGG
AGAAGTAAAGAAG

Alignment

ORF - retro_hsap_2471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 97.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SESSGADCKGDPRNSAKLDADYPLRVLYCGVCSLPTEYCEYMPDVAKCRQWLEKNFPNEFAKLTVENSPK
          SESSGADCKGDPRNSAKLDA.YPLRVLYCGVCSLPTEYCEYMPDVA.C.QWLEKNF.NE.AK.TVENSPK
Retrocopy SESSGADCKGDPRNSAKLDANYPLRVLYCGVCSLPTEYCEYMPDVAHCKQWLEKNFLNELAKFTVENSPK

Parental  QEAGISEGQGTAGEEEEKKKQKRGGRGQIKQKKKTVPQKVTIAKIPRAKKKYVTRVCGLATFEIDLKEAQ
          QEAGISEGQGTAGEEE....................PQK.T.AKIPRAKKK.VTRVCGLATFEIDLKEAQ
Retrocopy QEAGISEGQGTAGEEEXXXXXXXXXXXXXXXXXXXIPQKLTKAKIPRAKKKHVTRVCGLATFEIDLKEAQ

Parental  RF-FAQKFSCGASV-TGEDEIIIQGDFTDDIIDVIQ-EKWPEVDDDSIEDLGEVKK
          RF.FAQKFSC.ASV..GEDE.II.GDFTDDII.VIQ.EKWPEVDDDSI.DLGEVKK
Retrocopy RF<FAQKFSCAASV<NGEDE-IIRGDFTDDIIHVIQ<EKWPEVDDDSIKDLGEVKK

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	63.75 RPM
bodymap2_adrenal	0.00 RPM	53.96 RPM
bodymap2_brain	0.12 RPM	56.75 RPM
bodymap2_breast	0.06 RPM	90.70 RPM
bodymap2_colon	0.02 RPM	73.48 RPM
bodymap2_heart	0.30 RPM	34.73 RPM
bodymap2_kidney	0.04 RPM	70.09 RPM
bodymap2_liver	0.11 RPM	27.12 RPM
bodymap2_lung	0.00 RPM	35.07 RPM
bodymap2_lymph_node	0.93 RPM	51.97 RPM
bodymap2_ovary	0.13 RPM	81.56 RPM
bodymap2_prostate	0.17 RPM	76.07 RPM
bodymap2_skeletal_muscle	0.38 RPM	32.08 RPM
bodymap2_testis	0.23 RPM	78.77 RPM
bodymap2_thyroid	0.02 RPM	80.48 RPM
bodymap2_white_blood_cells	0.69 RPM	83.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2471 was not detected

EST

No EST(s) were mapped for retro_hsap_2471 retrocopy.

TSS

No TSS is located nearby retro_hsap_2471 retrocopy 5' end.

Lab

retro_hsap_2471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2471 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665, retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Homo sapiens	ENSG00000139726	4 retrocopies	retro_hsap_1028, retro_hsap_1854, retro_hsap_2471 , retro_hsap_4313,
Gorilla gorilla	ENSGGOG00000005562	3 retrocopies	retro_ggor_2156, retro_ggor_2883, retro_ggor_813,
Nomascus leucogenys	ENSNLEG00000002186	3 retrocopies	retro_nleu_1465, retro_nleu_2136, retro_nleu_906,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Ochotona princeps	ENSOPRG00000015974	5 retrocopies	retro_opri_1000, retro_opri_1139, retro_opri_1147, retro_opri_133, retro_opri_183,
Pongo abelii	ENSPPYG00000005073	3 retrocopies	retro_pabe_1821, retro_pabe_3509, retro_pabe_861,
Pan troglodytes	ENSPTRG00000005584	4 retrocopies	retro_ptro_1236, retro_ptro_2921, retro_ptro_2955, retro_ptro_703,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.24 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.38 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.27 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.32 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.19 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.15 RPM
GBR_HG00114	0.16 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.20 RPM
GBR_HG00133	0.22 RPM
GBR_HG00134	0.20 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.39 RPM
TSI_NA20518	0.25 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.32 RPM
TSI_NA20765	0.15 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.34 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.24 RPM
YRI_NA18916	0.19 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.29 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.20 RPM
YRI_NA19223	0.22 RPM

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Indel association:

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