RetrogeneDB ID: retro_cfam_1060

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:2269116..2269345(-)
• Located in intron of: ENSCAFG00000004341

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPG
• Ensembl ID: ENSCAFG00000032595
• Aliases: None
• Description: Canis lupus familiaris small nuclear ribonucleoprotein polypeptide G (SNRPG), mRNA. [Source:RefSeq mRNA;Acc:NM_001252331]

Sequence

>retro_cfam_1060
ATGAGTAAAGGTTACCAGCCCAATTGAAAAAAAAAGTATAGACAGGGAGTTATCACTGAAATTGAATAGTGGCAAACATG
GCTAAGCAGTATTGCAGGGATTTGGTTCCTTTATGAATCTGGCAGTAGATGAATGTGTGGAGATGGGAGCTAGTGGGCAA
TACAACAGTATTGGAATGGTGGTAATTGGATAAGATCATATCATGTTAGATTTAGAAGCCTTGAACAAG

Alignment

ORF - retro_cfam_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.25 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKAHPPELKKF-MDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIM
          MSK...P.......D..LSLKLN.G.H....L.GF..FMNL..DECVEM..SGQ.N.IGMVVI....I..
Retrocopy MSKGYQPNXXXX>IDRELSLKLNSGKHG*AVLQGFGSFMNLAVDECVEMGASGQYNSIGMVVIG*DHIML

Parental  -LEALER
          .LEAL..
Retrocopy DLEALNK

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	0.38 RPM	10.29 RPM
SRP017611_brain	0.16 RPM	2.78 RPM
SRP017611_kidney	0.26 RPM	21.79 RPM
SRP017611_liver	0.44 RPM	3.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1060 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1060 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_410

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 219 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032595	14 retrocopies	retro_cfam_1060 , retro_cfam_1458, retro_cfam_1871, retro_cfam_1984, retro_cfam_2210, retro_cfam_279, retro_cfam_306, retro_cfam_313, retro_cfam_407, retro_cfam_505, retro_cfam_817, retro_cfam_956, retro_cfam_967, retro_cfam_991,
Callithrix jacchus	ENSCJAG00000019313	18 retrocopies	retro_cjac_1034, retro_cjac_1227, retro_cjac_1398, retro_cjac_149, retro_cjac_1897, retro_cjac_223, retro_cjac_2419, retro_cjac_2431, retro_cjac_2658, retro_cjac_2795, retro_cjac_3246, retro_cjac_3314, retro_cjac_4078, retro_cjac_547, retro_cjac_763, retro_cjac_796, retro_cjac_897, retro_cjac_998,
Cavia porcellus	ENSCPOG00000025022	6 retrocopies	retro_cpor_1323, retro_cpor_145, retro_cpor_531, retro_cpor_573, retro_cpor_673, retro_cpor_843,
Equus caballus	ENSECAG00000019989	5 retrocopies	retro_ecab_1080, retro_ecab_197, retro_ecab_376, retro_ecab_410, retro_ecab_693,
Felis catus	ENSFCAG00000008118	8 retrocopies	retro_fcat_1006, retro_fcat_1092, retro_fcat_1248, retro_fcat_1467, retro_fcat_1893, retro_fcat_562, retro_fcat_82, retro_fcat_90,
Homo sapiens	ENSG00000143977	12 retrocopies	retro_hsap_1187, retro_hsap_1267, retro_hsap_1413, retro_hsap_1784, retro_hsap_1943, retro_hsap_1968, retro_hsap_2139, retro_hsap_2241, retro_hsap_2392, retro_hsap_296, retro_hsap_3786, retro_hsap_810,
Loxodonta africana	ENSLAFG00000002301	3 retrocopies	retro_lafr_428, retro_lafr_559, retro_lafr_887,
Microcebus murinus	ENSMICG00000015369	10 retrocopies	retro_mmur_1419, retro_mmur_1468, retro_mmur_1550, retro_mmur_265, retro_mmur_395, retro_mmur_59, retro_mmur_595, retro_mmur_625, retro_mmur_735, retro_mmur_901,
Myotis lucifugus	ENSMLUG00000026490	3 retrocopies	retro_mluc_273, retro_mluc_46, retro_mluc_731,
Macaca mulatta	ENSMMUG00000007961	3 retrocopies	retro_mmul_1021, retro_mmul_2048, retro_mmul_300,
Monodelphis domestica	ENSMODG00000011528	1 retrocopy	retro_mdom_1945,
Mustela putorius furo	ENSMPUG00000007221	2 retrocopies	retro_mputfur_100, retro_mputfur_114,
Mus musculus	ENSMUSG00000057278	1 retrocopy	retro_mmus_186,
Nomascus leucogenys	ENSNLEG00000010182	1 retrocopy	retro_nleu_93,
Oryctolagus cuniculus	ENSOCUG00000011214	2 retrocopies	retro_ocun_1032, retro_ocun_57,
Otolemur garnettii	ENSOGAG00000015300	13 retrocopies	retro_ogar_1138, retro_ogar_1691, retro_ogar_1982, retro_ogar_2533, retro_ogar_2626, retro_ogar_2696, retro_ogar_2787, retro_ogar_3149, retro_ogar_3386, retro_ogar_351, retro_ogar_638, retro_ogar_745, retro_ogar_836,
Pongo abelii	ENSPPYG00000012324	14 retrocopies	retro_pabe_1054, retro_pabe_1078, retro_pabe_1079, retro_pabe_1169, retro_pabe_1188, retro_pabe_1465, retro_pabe_1603, retro_pabe_1728, retro_pabe_1929, retro_pabe_2041, retro_pabe_2160, retro_pabe_3093, retro_pabe_495, retro_pabe_95,
Pan troglodytes	ENSPTRG00000012029	11 retrocopies	retro_ptro_1194, retro_ptro_1297, retro_ptro_1314, retro_ptro_1565, retro_ptro_1585, retro_ptro_243, retro_ptro_2568, retro_ptro_563, retro_ptro_814, retro_ptro_867, retro_ptro_967,
Pteropus vampyrus	ENSPVAG00000004855	3 retrocopies	retro_pvam_612, retro_pvam_613, retro_pvam_666,
Rattus norvegicus	ENSRNOG00000016507	1 retrocopy	retro_rnor_409,
Ictidomys tridecemlineatus	ENSSTOG00000008654	11 retrocopies	retro_itri_1116, retro_itri_1260, retro_itri_128, retro_itri_1395, retro_itri_1871, retro_itri_280, retro_itri_353, retro_itri_572, retro_itri_589, retro_itri_910, retro_itri_947,
Tupaia belangeri	ENSTBEG00000017381	66 retrocopies	retro_tbel_1010, retro_tbel_1076, retro_tbel_1114, retro_tbel_1133, retro_tbel_1161, retro_tbel_1164, retro_tbel_1174, retro_tbel_121, retro_tbel_1288, retro_tbel_1448, retro_tbel_1461, retro_tbel_147, retro_tbel_1478, retro_tbel_149, retro_tbel_164, retro_tbel_1654, retro_tbel_1887, retro_tbel_1939, retro_tbel_1944, retro_tbel_1965, retro_tbel_1966, retro_tbel_1997, retro_tbel_2001, retro_tbel_2143, retro_tbel_217, retro_tbel_236, retro_tbel_239, retro_tbel_241, retro_tbel_2454, retro_tbel_2462, retro_tbel_2572, retro_tbel_2664, retro_tbel_2941, retro_tbel_3098, retro_tbel_3379, retro_tbel_3385, retro_tbel_343, retro_tbel_347, retro_tbel_3495, retro_tbel_3559, retro_tbel_3603, retro_tbel_362, retro_tbel_3699, retro_tbel_3980, retro_tbel_3981, retro_tbel_3983, retro_tbel_4010, retro_tbel_4011, retro_tbel_4177, retro_tbel_4196, retro_tbel_43, retro_tbel_4399, retro_tbel_4442, retro_tbel_4505, retro_tbel_4549, retro_tbel_4609, retro_tbel_465, retro_tbel_489, retro_tbel_697, retro_tbel_726, retro_tbel_736, retro_tbel_805, retro_tbel_921, retro_tbel_93, retro_tbel_936, retro_tbel_947,
Tarsius syrichta	ENSTSYG00000005729	11 retrocopies	retro_tsyr_1202, retro_tsyr_134, retro_tsyr_1440, retro_tsyr_1592, retro_tsyr_1747, retro_tsyr_2038, retro_tsyr_222, retro_tsyr_287, retro_tsyr_322, retro_tsyr_431, retro_tsyr_698,