RetrogeneDB ID: retro_cfam_965

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:41386619..41387107(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004560
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSCAFG00000000994
• Aliases: None
• Description: Canis lupus familiaris S-phase kinase-associated protein 1 (SKP1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252408]

Sequence

>retro_cfam_965
ATGCCTTCAATTAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTTGAAATTGCCAAACAGTCTGTGACTAT
CAAGACCATGTTGGAAGATTTGGGAATGGATGATGAAGGAGATGATGACCCAGTTCCTCTACCAAATGTTAACGCAGCAA
TATTAAAAAAGGTCATTCAGTGGTGCACCCGCCACAAGGATGACCCCCCTTCTCCTGAGGACAATGAGAACAAAGAAAAG
TGGACAGATGATATTCCTGTTTGGGACCAAGAATTCCTGAAAGTTGACCAAGGAACACTTTTTGAACTTATTCTGGCTGC
GAACTACTTAGACATCAAAGGTTTGCTTGATGTTACATGCAAGACTGTTGCCAATATGATCAAGGGGAAAACTCCTGAGG
AGATCGTAAGACCTTCAATATCAAAAATTACTTTACTGAAGAAGAGGAAGCCCAGGTACCCAAAGAGAACCAGTGGTGTG
AAGAGAAG

Alignment

ORF - retro_cfam_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLPSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPP
          MPSIKL.SSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCT.HKDDPP
Retrocopy MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTRHKDDPP

Parental  PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEI-RKTF
          .PED.ENKEK.TDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEI.RKTF
Retrocopy SPEDNENKEKWTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEI<RKTF

Parental  NIKNDFTEEEEAQVRKENQWCEEK
          NIKN.FTEEEEAQV.KENQWCEEK
Retrocopy NIKNYFTEEEEAQVPKENQWCEEK

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	14.49 RPM	161.15 RPM
SRP017611_brain	16.20 RPM	167.36 RPM
SRP017611_kidney	18.03 RPM	222.22 RPM
SRP017611_liver	3.48 RPM	38.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_965 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_965 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 173 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017810	1 retrocopy	retro_amel_897,
Bos taurus	ENSBTAG00000025191	5 retrocopies	retro_btau_10, retro_btau_1062, retro_btau_1253, retro_btau_1444, retro_btau_1687,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965 ,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Cavia porcellus	ENSCPOG00000005164	8 retrocopies	retro_cpor_1038, retro_cpor_1133, retro_cpor_1345, retro_cpor_1446, retro_cpor_223, retro_cpor_243, retro_cpor_830, retro_cpor_832,
Dasypus novemcinctus	ENSDNOG00000012999	9 retrocopies	retro_dnov_1216, retro_dnov_1338, retro_dnov_2433, retro_dnov_2526, retro_dnov_2647, retro_dnov_281, retro_dnov_286, retro_dnov_389, retro_dnov_776,
Dipodomys ordii	ENSDORG00000002912	3 retrocopies	retro_dord_338, retro_dord_512, retro_dord_720,
Equus caballus	ENSECAG00000003931	2 retrocopies	retro_ecab_466, retro_ecab_789,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Felis catus	ENSFCAG00000031140	1 retrocopy	retro_fcat_653,
Homo sapiens	ENSG00000113558	10 retrocopies	retro_hsap_2193, retro_hsap_2596, retro_hsap_3321, retro_hsap_3346, retro_hsap_3863, retro_hsap_4161, retro_hsap_4163, retro_hsap_4164, retro_hsap_724, retro_hsap_972,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Latimeria chalumnae	ENSLACG00000016599	1 retrocopy	retro_lcha_103,
Loxodonta africana	ENSLAFG00000016832	1 retrocopy	retro_lafr_83,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Macaca mulatta	ENSMMUG00000013046	7 retrocopies	retro_mmul_1171, retro_mmul_2082, retro_mmul_2091, retro_mmul_2508, retro_mmul_654, retro_mmul_795, retro_mmul_919,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Mus musculus	ENSMUSG00000036309	1 retrocopy	retro_mmus_2518,
Nomascus leucogenys	ENSNLEG00000008051	7 retrocopies	retro_nleu_1171, retro_nleu_1615, retro_nleu_1667, retro_nleu_2290, retro_nleu_323, retro_nleu_472, retro_nleu_827,
Oryctolagus cuniculus	ENSOCUG00000022505	10 retrocopies	retro_ocun_1119, retro_ocun_1228, retro_ocun_1242, retro_ocun_1420, retro_ocun_1453, retro_ocun_1572, retro_ocun_1784, retro_ocun_397, retro_ocun_448, retro_ocun_553,
Otolemur garnettii	ENSOGAG00000028707	8 retrocopies	retro_ogar_1446, retro_ogar_1510, retro_ogar_1511, retro_ogar_1890, retro_ogar_2019, retro_ogar_2728, retro_ogar_3306, retro_ogar_581,
Ochotona princeps	ENSOPRG00000006637	7 retrocopies	retro_opri_1199, retro_opri_188, retro_opri_23, retro_opri_513, retro_opri_547, retro_opri_902, retro_opri_955,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Pteropus vampyrus	ENSPVAG00000012427	4 retrocopies	retro_pvam_1040, retro_pvam_1137, retro_pvam_1269, retro_pvam_503,
Rattus norvegicus	ENSRNOG00000005828	6 retrocopies	retro_rnor_1391, retro_rnor_1392, retro_rnor_1465, retro_rnor_1888, retro_rnor_2166, retro_rnor_2333,
Sorex araneus	ENSSARG00000008307	4 retrocopies	retro_sara_241, retro_sara_446, retro_sara_492, retro_sara_609,
Tupaia belangeri	ENSTBEG00000015544	15 retrocopies	retro_tbel_1227, retro_tbel_1279, retro_tbel_1327, retro_tbel_1758, retro_tbel_1787, retro_tbel_1903, retro_tbel_1905, retro_tbel_240, retro_tbel_3024, retro_tbel_3267, retro_tbel_3848, retro_tbel_405, retro_tbel_4095, retro_tbel_528, retro_tbel_711,
Tarsius syrichta	ENSTSYG00000010696	11 retrocopies	retro_tsyr_1037, retro_tsyr_1370, retro_tsyr_1400, retro_tsyr_1896, retro_tsyr_1924, retro_tsyr_2058, retro_tsyr_210, retro_tsyr_336, retro_tsyr_396, retro_tsyr_464, retro_tsyr_762,
Tursiops truncatus	ENSTTRG00000016858	6 retrocopies	retro_ttru_1344, retro_ttru_1764, retro_ttru_1801, retro_ttru_656, retro_ttru_657, retro_ttru_961,
Vicugna pacos	ENSVPAG00000001583	1 retrocopy	retro_vpac_279,