RetrogeneDB ID: retro_hsap_3522

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:135219376..135219891(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSG00000162959
• Aliases: MEMO1, C2orf4, MEMO, NS5ATP7
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_hsap_3522
GTCTCTGCAGACAAAGATGAACACGGTATTGAAATGCATTTGCCTTGTACAGCTAAAGCCATGGAAATCCATAAGGATGA
GTTTACCATTATTCCTGTACTGGTTGGAGCTCTGAGTGAGTCAAAAGAACAGGAATTCGGAAAACTCTTCAGTAAATATC
TAGCAGATCCTAGTAATTTCTTTGTGGTTTCTTCTGATTTTTGCCATTGGGGTCAAAGATTCCGTTACAGTTACTATGAT
GAATCCCAGGGGGAGACTTATAGATCCATTGAACATCTAGATAAAATGGGTATGAGTATTATAGAACAATTAGACCCTGT
ATCTTTTAGCAATTACTTGAGGAAACACCATAATACTATATGTGGAAGACATCCCTTTAGGGTGTTAAATGCTATCACAG
AGCTCCAGAAGAATGGAAGAATATGAGCTTTTCCTTTTTGAATTATGCCCAGTCAAGCCAGTGTAGAAACTGGCAAGACA
GTTCAGTGAGTTACACAACTGGAGCGCTCACGGTC

Alignment

ORF - retro_hsap_3522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 58.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHW
          ...D.DEH.IEMHLP.TAKAME.HKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSN.FVVSSDFCHW
Retrocopy VSADKDEHGIEMHLPCTAKAMEIHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNFFVVSSDFCHW

Parental  GQRFRYSYYDESQGEIYRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNG
          GQRFRYSYYDESQGE.YRSIEHLDKMGMSIIEQLDPVSFSNYL.K.HNTICGRHP..V.LNAITELQKNG
Retrocopy GQRFRYSYYDESQGETYRSIEHLDKMGMSIIEQLDPVSFSNYLRKHHNTICGRHPFRV-LNAITELQKNG

Parental  -MNMSFSFLNYAQSSQCRNWQDSSVSYAAGALTV
          ..NMSFSFLNYAQSSQCRNWQDSSVSY..GALTV
Retrocopy <KNMSFSFLNYAQSSQCRNWQDSSVSYTTGALTV

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	0.44 RPM
bodymap2_adrenal	0.02 RPM	0.88 RPM
bodymap2_brain	0.07 RPM	0.75 RPM
bodymap2_breast	0.00 RPM	0.47 RPM
bodymap2_colon	0.00 RPM	0.23 RPM
bodymap2_heart	0.00 RPM	0.39 RPM
bodymap2_kidney	0.12 RPM	0.12 RPM
bodymap2_liver	0.04 RPM	0.40 RPM
bodymap2_lung	0.00 RPM	0.44 RPM
bodymap2_lymph_node	0.00 RPM	0.27 RPM
bodymap2_ovary	0.00 RPM	0.19 RPM
bodymap2_prostate	0.00 RPM	0.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.49 RPM
bodymap2_testis	0.08 RPM	1.45 RPM
bodymap2_thyroid	0.00 RPM	0.38 RPM
bodymap2_white_blood_cells	0.00 RPM	0.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3522 was not detected

EST

No EST(s) were mapped for retro_hsap_3522 retrocopy.

TSS

No TSS is located nearby retro_hsap_3522 retrocopy 5' end.

Lab

retro_hsap_3522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3522 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2910

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522 ,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 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	0.03 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	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 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	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 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).