RetrogeneDB ID: retro_cfam_254

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:33795726..33796097(+)
• Located in intron of: ENSCAFG00000000294

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSCAFG00000004533
• Aliases: None
• Description: tumor protein, translationally-controlled 1 [Source:HGNC Symbol;Acc:12022]

Sequence

>retro_cfam_254
GATGAGCCACTCATTGCTGAAAATGCCTTTACTGAAGGCCCTGGGGGAAAGGTATCCAACACACAGTCATCCCTGGTGTT
GATATTGTCACGAACTATCACTTGTAAGAGACCAAATTCACAAAAGAAGCCTACAAGTAGTACATCAAAGATTGTATGAA
ATCAATCAAAGGGAAACTTAAAGAACAGTATCAAAAAGAGTAAAATTTTTTATGACAGGGGCTACAGAAAAAAATCAAGC
ACATGCTTGCTAATTTCAAAAACTACCAATTCTTTCTTGGTAAAAACATGAATCCAGATGACATGGTTTTTATCCTGGAC
TACCATGAAGATGGTGTGAGCTCATATGTGATTTATTTGAAGGCTGGTTTA

Alignment

ORF - retro_cfam_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDSLIGGNASAEGPEGE-GTESTVITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPE-RV
          D..LI..NA..EGP.G..G...TVI.GVDIV.N.HL.ET.FTKEAYK.YIKD.MKSIKGKL.EQ....RV
Retrocopy DEPLIAENAFTEGPGGK<GIQHTVIPGVDIVTNYHL*ETKFTKEAYK*YIKDCMKSIKGKLKEQYQK<RV

Parental  KPFMTGAAEQ-IKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGL
          K.FMTGA.E..IKH.LANFKNYQFF.G.NMNPD.MV..LDY.EDGV..Y.I..K.GL
Retrocopy KFFMTGATEK>IKHMLANFKNYQFFLGKNMNPDDMVFILDYHEDGVSSYVIYLKAGL

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	0.00 RPM	463.88 RPM
SRP017611_brain	0.00 RPM	234.37 RPM
SRP017611_kidney	0.00 RPM	1876.97 RPM
SRP017611_liver	0.00 RPM	989.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_254 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Ailuropoda melanoleuca	ENSAMEG00000013022	8 retrocopies	retro_amel_1153, retro_amel_1521, retro_amel_1593, retro_amel_1804, retro_amel_1878, retro_amel_472, retro_amel_569, retro_amel_969,
Canis familiaris	ENSCAFG00000004533	10 retrocopies	retro_cfam_1110, retro_cfam_1328, retro_cfam_1476, retro_cfam_1508, retro_cfam_1846, retro_cfam_254 , retro_cfam_341, retro_cfam_483, retro_cfam_661, retro_cfam_777,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Equus caballus	ENSECAG00000018348	3 retrocopies	retro_ecab_337, retro_ecab_686, retro_ecab_727,
Felis catus	ENSFCAG00000002107	8 retrocopies	retro_fcat_1366, retro_fcat_1544, retro_fcat_1996, retro_fcat_443, retro_fcat_553, retro_fcat_645, retro_fcat_735, retro_fcat_992,
Homo sapiens	ENSG00000133112	13 retrocopies	retro_hsap_1083, retro_hsap_2234, retro_hsap_2256, retro_hsap_2382, retro_hsap_2503, retro_hsap_3156, retro_hsap_3676, retro_hsap_3828, retro_hsap_3946, retro_hsap_4307, retro_hsap_4701, retro_hsap_4786, retro_hsap_678,
Gorilla gorilla	ENSGGOG00000001684	12 retrocopies	retro_ggor_1561, retro_ggor_1681, retro_ggor_1807, retro_ggor_2045, retro_ggor_2484, retro_ggor_2628, retro_ggor_2652, retro_ggor_2877, retro_ggor_2878, retro_ggor_2980, retro_ggor_584, retro_ggor_855,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Microcebus murinus	ENSMICG00000002027	9 retrocopies	retro_mmur_102, retro_mmur_1060, retro_mmur_1163, retro_mmur_1627, retro_mmur_248, retro_mmur_318, retro_mmur_490, retro_mmur_641, retro_mmur_967,
Macaca mulatta	ENSMMUG00000022979	2 retrocopies	retro_mmul_158, retro_mmul_85,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Mustela putorius furo	ENSMPUG00000001640	10 retrocopies	retro_mputfur_1043, retro_mputfur_30, retro_mputfur_364, retro_mputfur_565, retro_mputfur_574, retro_mputfur_582, retro_mputfur_677, retro_mputfur_870, retro_mputfur_960, retro_mputfur_967,
Procavia capensis	ENSPCAG00000016228	3 retrocopies	retro_pcap_245, retro_pcap_351, retro_pcap_357,
Pongo abelii	ENSPPYG00000005335	5 retrocopies	retro_pabe_1958, retro_pabe_2626, retro_pabe_2809, retro_pabe_83, retro_pabe_900,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,
Ictidomys tridecemlineatus	ENSSTOG00000006931	7 retrocopies	retro_itri_1192, retro_itri_146, retro_itri_266, retro_itri_325, retro_itri_612, retro_itri_700, retro_itri_999,