RetrogeneDB ID: retro_cfam_88

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:33110990..33111566(-)
• Located in intron of: ENSCAFG00000017520

Retrocopy information

• Ensembl ID: ENSCAFG00000017518
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CDC42
• Ensembl ID: ENSCAFG00000014707
• Aliases: None
• Description: Canis lupus familiaris cell division cycle 42 (GTP binding protein, 25kDa) (CDC42), mRNA. [Source:RefSeq mRNA;Acc:NM_001003254]

Sequence

>retro_cfam_88
ATGCAGACAACTGAGTGCATTGTTGTGGGCGATGGTGCCATTGGTAAAACATGTCTCCTGATATCCTACACAACAAACAA
ATTTCCATCTGAGTATGTACCGACTGTTTTTGACAACTATGCAGTCACAGTTATGATTGGTGGAGAGCCACATACCCTTG
GACTTTCTGATACTGCAGGGCAAGAGGATTATGACAGATTACAACTGCTGAGTTATCCACAAACAGATGTATTTCGAGTC
TGTTTTTCAGTGTTCTCTCCATCCTCATTTGAAAATGTGAAGGAAAAGTGGGTGCCTGAGATAACTCACCACTGTCCAAA
GACTCCTTTCTTGCTTGTTAGGACCCAAATTGATCTCCGAGATGACCCCTCTACTATTGAGAAACCTGCCAAGAACAAAC
AGAAGCCTATCACTCCAGAGACTGCTGAAAAGCTGGCCTGTGACCTGAAGGCGGTCAAGTATGTGGAGTGTTCTGCACTC
ACAGAGAAAGGCCTAAAGAATGTATTTGACGAAGGAATATTGGCTGCCCTGGAGCCTCCAGAACCGAAGAAGAGCCGCAG
GTGTGTGCTGCTATGA

Alignment

ORF - retro_cfam_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPL
          MQT..C.VVGDGA.GKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEP.TLGL.DTAGQEDYDRL..L
Retrocopy MQTTECIVVGDGAIGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPHTLGLSDTAGQEDYDRLQLL

Parental  SYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPE
          SYPQTDVF.VCFSV.SPSSFENVKEKWVPEITHHCPKTPFLLV.TQIDLRDDPSTIEK.AKNKQKPITPE
Retrocopy SYPQTDVFRVCFSVFSPSSFENVKEKWVPEITHHCPKTPFLLVRTQIDLRDDPSTIEKPAKNKQKPITPE

Parental  TAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL
          TAEKLA.DLKAVKYVECSALT.KGLKNVFDE.ILAALEPPEPKKSRRCVLL
Retrocopy TAEKLACDLKAVKYVECSALTEKGLKNVFDEGILAALEPPEPKKSRRCVLL

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
SRP012049_cerebellum	0.13 RPM	39.65 RPM
SRP017611_brain	0.00 RPM	32.15 RPM
SRP017611_kidney	0.20 RPM	27.67 RPM
SRP017611_liver	0.00 RPM	5.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_88 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_88 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 122 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,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
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,
Dipodomys ordii	ENSDORG00000010374	3 retrocopies	retro_dord_17, retro_dord_464, retro_dord_552,
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,
Homo sapiens	ENSG00000070831	6 retrocopies	retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Gorilla gorilla	ENSGGOG00000024439	5 retrocopies	retro_ggor_1932, retro_ggor_2057, retro_ggor_2303, retro_ggor_2593, retro_ggor_2695,
Myotis lucifugus	ENSMLUG00000013365	4 retrocopies	retro_mluc_1076, retro_mluc_1864, retro_mluc_2456, retro_mluc_905,
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,
Nomascus leucogenys	ENSNLEG00000008198	4 retrocopies	retro_nleu_2029, retro_nleu_2949, retro_nleu_3007, retro_nleu_679,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Ochotona princeps	ENSOPRG00000005331	2 retrocopies	retro_opri_868, retro_opri_995,
Pongo abelii	ENSPPYG00000001755	6 retrocopies	retro_pabe_2240, retro_pabe_2461, retro_pabe_2801, retro_pabe_3215, retro_pabe_3239, retro_pabe_3295,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Sus scrofa	ENSSSCG00000003520	1 retrocopy	retro_sscr_899,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,
Tupaia belangeri	ENSTBEG00000002614	17 retrocopies	retro_tbel_1091, retro_tbel_1379, retro_tbel_1697, retro_tbel_1711, retro_tbel_183, retro_tbel_2320, retro_tbel_2447, retro_tbel_2721, retro_tbel_4016, retro_tbel_4168, retro_tbel_4184, retro_tbel_4273, retro_tbel_4427, retro_tbel_584, retro_tbel_585, retro_tbel_860, retro_tbel_873,
Tarsius syrichta	ENSTSYG00000000679	11 retrocopies	retro_tsyr_1575, retro_tsyr_1597, retro_tsyr_1854, retro_tsyr_1976, retro_tsyr_2048, retro_tsyr_2098, retro_tsyr_352, retro_tsyr_387, retro_tsyr_539, retro_tsyr_66, retro_tsyr_963,
Tursiops truncatus	ENSTTRG00000005708	2 retrocopies	retro_ttru_118, retro_ttru_54,
Vicugna pacos	ENSVPAG00000006919	3 retrocopies	retro_vpac_13, retro_vpac_451, retro_vpac_542,