RetrogeneDB ID: retro_pabe_2801

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:175742582..175743077(-)
• Located in intron of: ENSPPYG00000016053

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC42
• Ensembl ID: ENSPPYG00000001755
• Aliases: None
• Description: cell division cycle 42 [Source:HGNC Symbol;Acc:1736]

Sequence

>retro_pabe_2801
ATGCAGATAATTAAGTGTGTTGTGGGTGATAGTGCTGTTGGCAAAAAATGTCTCCTGATATCCTACACGACAAACAAATT
ACCATCGGAATAACGTACTGTTTTTGACAACTATGCAGTCACAGTTATGACTGGTAGAGAACCATACACTCTTGGATTTT
TGATACTGCAGGGCAAAGGTTTATGACAGATTATGACTGCTGAGTTATCCACAAACAGATGTATTTCTAGTCTGTTTTTC
AGTGGTCTCTCCATCTTCATTTGAAAATGTGAAAAAAAGTGGGTGCCTGAGATAACTGTCCCAAAGACTCCTTTCTTGCT
TGTTGGGACCCAAACTGATCTCAGAGATGATCCCTCTACTATTGAGAAACTTGCCAAGAACAAACAGAAGCCTATCACTC
TGGAGACTGCTAAAAAGCTGGCCCGTGACCTGAAGGCCGTCAGGTATGTGGAGTGTTTTACACTCACACAGAAAGGCCTA
AAGAATGTATTTGAC

Alignment

ORF - retro_pabe_2801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.82 %
• Parental protein coverage: 89.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLG-LFDTAGQ-EDYDRLR
          MQ.IKCVV.GD.AVGK.CLLISYTTNK.PSE...TVFDNYAVTVM.G.EPYTLG..FDTAGQ...YDRL.
Retrocopy MQIIKCVV-GDSAVGKKCLLISYTTNKLPSE*-RTVFDNYAVTVMTGREPYTLG<IFDTAGQ<KVYDRL*

Parental  PLSYPQTDVFLVCFSVVSPSSFENVKE-KWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPI
          .LSYPQTDVFLVCFSVVSPSSFENVK..KWVPEIT...PKTPFLLVGTQ.DLRDDPSTIEKLAKNKQKPI
Retrocopy LLSYPQTDVFLVCFSVVSPSSFENVKK<KWVPEIT--VPKTPFLLVGTQTDLRDDPSTIEKLAKNKQKPI

Parental  TPETAEKLARDLKAVKYVECSALTQKGLKNVFD
          T.ETA.KLARDLKAV.YVEC..LTQKGLKNVFD
Retrocopy TLETAKKLARDLKAVRYVECFTLTQKGLKNVFD

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	0.06 RPM	56.18 RPM
SRP007412_cerebellum	0.12 RPM	63.11 RPM
SRP007412_heart	0.03 RPM	45.03 RPM
SRP007412_kidney	0.03 RPM	103.42 RPM
SRP007412_liver	0.03 RPM	72.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2801 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2801 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3404
Gorilla gorilla	retro_ggor_2303
Callithrix jacchus	retro_cjac_1808

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus	ENSECAG00000019180	1 retrocopy	retro_ecab_11,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Gorilla gorilla	ENSGGOG00000024439	5 retrocopies	retro_ggor_1932, retro_ggor_2057, retro_ggor_2303, retro_ggor_2593, retro_ggor_2695,
Macaca mulatta	ENSMMUG00000022009	8 retrocopies	retro_mmul_1449, retro_mmul_1612, retro_mmul_1685, retro_mmul_1900, retro_mmul_1932, retro_mmul_24, retro_mmul_349, retro_mmul_598,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Mus musculus	ENSMUSG00000006699	3 retrocopies	retro_mmus_2816, retro_mmus_2995, retro_mmus_3170,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801 , retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,