RetrogeneDB ID: retro_pabe_2910

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:137814197..137814712(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSPPYG00000012511
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_pabe_2910
GTCTCTGCAGACAAAGATGAACACAGTATTGAAATGCATTTGCCTTATAGAGCTAAAGCCATGGAAATCCATAAGGATGA
GTTTACCATTATTCCTGTACGGGTTGGAGCTCTGAGCGAGTCAAAAGAACAGGAATTCAGAAAACTCTTCAGTAAATATC
TAGCAGATCCTAGTAATTTCTTTGTGGTTTCTTCTGATTTTTGCCATTGGGATCAAAGATTCCGTTACGGTTACTATGAT
GAATCCCAGGGGGAGACTTATAGATCCATTGAACATCTAGATAAAATGGGTATGAGTATTATAGAACAATTAGACCCTGT
ATCTATTAGCAATTACTTGAGGAAACACCATAATATTATATGTGGAAGACATCGCTTTAGGGTGTTAAATGCTATCACAG
AGCTCCAGAAGAATGGAAGAATATGAGCTTTTCCTTTTTGAATTATGCCCAGTCAAGCCAGTGTAGAAACTGGCAAGACA
GTTCAGTGAGTTACACAACTGGAGCACTCACAGTC

Alignment

ORF - retro_pabe_2910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 62.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHW
          ...D.DEHSIEMHLPY.AKAME.HKDEFTIIPV.VGALSESKEQEF.KLFSKYLADPSN.FVVSSDFCHW
Retrocopy VSADKDEHSIEMHLPYRAKAMEIHKDEFTIIPVRVGALSESKEQEFRKLFSKYLADPSNFFVVSSDFCHW

Parental  GQRFRYSYYDESQGEIYRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNG
          .QRFRY.YYDESQGE.YRSIEHLDKMGMSIIEQLDPVS.SNYL.K.HN.ICGRH...V.LNAITELQKNG
Retrocopy DQRFRYGYYDESQGETYRSIEHLDKMGMSIIEQLDPVSISNYLRKHHNIICGRHRFRV-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
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.51 RPM
SRP007412_cerebellum	0.00 RPM	7.05 RPM
SRP007412_heart	0.00 RPM	8.04 RPM
SRP007412_kidney	0.00 RPM	10.14 RPM
SRP007412_liver	0.00 RPM	8.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2910 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2910 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3522

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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 ,