RetrogeneDB ID: retro_hsap_634

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:121380579..121381211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234569
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSG00000113456
• Aliases: RAD1, HRAD1, REC1
• Description: RAD1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9806]

Sequence

>retro_hsap_634
ATGCCCCTCCTGACCCAACAGATCCAAGACGAGCATGATCAATACAGTCTTGTGGCCAGCCTTGACAATGTTAGGAATCT
CTCCACTATCTTAAAAGCTATTCATTTCCGAAAATGTGCTGTGTGTTTCGCAACTAAAAATGGAATCAAAGTAACAATGG
AAAATGCAAAGTGTGTGCAAGCAAATGCTTTTATTCAGGCTGGAATATTTCAAGAGCTTAAAGTTCAGGAAGAGTCTGTT
ACTTTTTGAATTAATTTCATTGTCCTTTTAGACTGTTTATCTATTTTTGGATCAAGTCCTATGCCAGGGACTTGAACTGC
ACTTCGGATGTGTTACCAAGGTTATGGTTACCCTTTGATGCTGTTCCTGGAAGAAGAAGGAGTGGTGGCAGTCTGCAAAA
TCAATACACAGGAACCTGAAGGGACCTGGACTTTAATTTCTACAGCACTAATGTTATTGATAAAATTCTGCAGTCAGAAG
GGCTCTGTGAAGCTTTTTCTGAATTGGATATGACGAGTGAGGTCCTACAAATTACCATGTCTCCTGACAAGCCTTATTTC
AGGTTATCTACTTTTGGAAATGTAGGAAGTTCCCACCTTGACCGCCCCAAAGATTCTGATTTGATGGAAGCA

Alignment

ORF - retro_hsap_634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 75.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLLTQQIQDEDDQYSLVASLDNVRNLSTILKAIHFREHATCFATKNGIKVTVENAKCVQANAFIQAGIF
          MPLLTQQIQDE.DQYSLVASLDNVRNLSTILKAIHFR..A.CFATKNGIKVT.ENAKCVQANAFIQAGIF
Retrocopy MPLLTQQIQDEHDQYSLVASLDNVRNLSTILKAIHFRKCAVCFATKNGIKVTMENAKCVQANAFIQAGIF

Parental  QEFKVQEESVTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLMLFLEEGGVVTVCKINTQEPE
          QE.KVQEESVTF.IN..VLLDCLSIFGSSPMPGT.TALRMCYQGYGYPLMLFLEE.GVV.VCKINTQEPE
Retrocopy QELKVQEESVTF*INFIVLLDCLSIFGSSPMPGT*TALRMCYQGYGYPLMLFLEEEGVVAVCKINTQEPE

Parental  ET-LDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQITMSPDKPYFRLSTFGNAGSSHLDYPKDSDL
          .T.LDF.F.STNVI.K.ILQSEGL.EAFSELDMTSEVLQITMSPDKPYFRLSTFGN.GSSHLD.PKDSDL
Retrocopy GT<LDFNFYSTNVIDK-ILQSEGLCEAFSELDMTSEVLQITMSPDKPYFRLSTFGNVGSSHLDRPKDSDL

Parental  MEA
          MEA
Retrocopy MEA

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	14.91 RPM
bodymap2_adrenal	0.00 RPM	28.90 RPM
bodymap2_brain	0.09 RPM	26.16 RPM
bodymap2_breast	0.00 RPM	16.85 RPM
bodymap2_colon	0.00 RPM	23.13 RPM
bodymap2_heart	0.00 RPM	31.20 RPM
bodymap2_kidney	0.00 RPM	28.29 RPM
bodymap2_liver	0.00 RPM	9.49 RPM
bodymap2_lung	0.00 RPM	20.20 RPM
bodymap2_lymph_node	0.00 RPM	29.66 RPM
bodymap2_ovary	0.00 RPM	35.18 RPM
bodymap2_prostate	0.00 RPM	30.73 RPM
bodymap2_skeletal_muscle	0.00 RPM	22.41 RPM
bodymap2_testis	0.09 RPM	42.97 RPM
bodymap2_thyroid	0.00 RPM	34.18 RPM
bodymap2_white_blood_cells	0.00 RPM	23.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_634 was not detected

EST

No EST(s) were mapped for retro_hsap_634 retrocopy.

TSS

No TSS is located nearby retro_hsap_634 retrocopy 5' end.

Lab

retro_hsap_634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_634 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_462
Gorilla gorilla	retro_ggor_555
Pongo abelii	retro_pabe_564
Callithrix jacchus	retro_cjac_1004

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634 ,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738,

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	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 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	0.02 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	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 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	0.00 RPM

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Indel association:

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