RetrogeneDB ID: retro_pabe_2461

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:114222995..114223340(+)
• Located in intron of: ENSPPYG00000029772

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_2461
ACAGATGTATTTCTAGTCTGTTTCTCAGTGGTCTCTCCATGTTCATTTTAAAGTATGAAAGAAAAGTGAGGGCCTGAGAT
AACTCACCACTGTCCAAAGGCTCCTTTCTTGCTTGTCACGACCCAAACTGATCTCAGAGGGTCTATTATTGAGAAAATTA
CCAAGAACAAACAGAAGCCTATCACTCCAGAGACTGCTGAAAAGCCGGCCCACAACCTGAAGGCTGTCAAGTATATGGAT
GGTCCTGTACCCACACAGCAAGACCTAAAGAATGGATTGGACAAAGCAATATTGGCTATCCTGGAGCCTCCAGAACTGAA
GAAGAGCTGCAAGCCTATGCTGCTA

Alignment

ORF - retro_pabe_2461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 61.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEK
          TDVFLVCFSVVSP.SF...KEK..PEITHHCPK.PFLLV.TQ.DLR...S.IEK..KNKQKPITPETAEK
Retrocopy TDVFLVCFSVVSPCSF*SMKEK*GPEITHHCPKAPFLLVTTQTDLRG--SIIEKITKNKQKPITPETAEK

Parental  LARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL
          .A..LKAVKY......TQ..LKN..D.AILA.LEPPE.KKS....LL
Retrocopy PAHNLKAVKYMDGPVPTQQDLKNGLDKAILAILEPPELKKSCKPMLL

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	0.49 RPM	63.11 RPM
SRP007412_heart	0.00 RPM	45.03 RPM
SRP007412_kidney	0.17 RPM	103.42 RPM
SRP007412_liver	0.06 RPM	72.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2461 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2461 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2968
Gorilla gorilla	retro_ggor_2057
Macaca mulatta	retro_mmul_1900

---

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,