RetrogeneDB ID: retro_cfam_1

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:13211789..13212287(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011435
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSCAFG00000001214
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein S10 (RPS10), mRNA. [Source:RefSeq mRNA;Acc:NM_001252045]

Sequence

>retro_cfam_1
ATGTTGATGCCCAAGAAGAACCAAATCGCCATTTATGAACTCCTTTTCAAGGAGGGGGTGATGGTGGCAAAGAAGGACGT
CCACATGCCCAAACACCCTGAACTGGCCGACAAGAATGTGCCCAACCTTCACGTCATGAAGGCCATGCAGTCTCTCAAAT
CCCGAGGCTACGTAAAGGAACAGTTTGCTTGGAGACATTTCTACTGGTACCTTACCAACGAGGGTATCCAGTATCTCCGT
GATTACCTCCACCTACCCCCCGAGATTGTGCCTGCCACTCTGCGCCGCAGCAGACCGGAGACCGGCAGGCCACGGCCCAA
AGGTCTGGAGGGAGAGCGACCTGCAAGACTGACACGAGGGGAAGCTGACAGAGACACCTACAGACGAAGCGCTGTGCCCC
CTGGTGCCGACAAGAAAGCTGAGGCTGGGGCAGGGTCAGCAACAGAGTTCCAGTTTAGAGGCGGATTTGGTCGTGGACGT
GGTCAGCCACCTCAGTAA

Alignment

ORF - retro_cfam_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
          MLMPKKN.IAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
Retrocopy MLMPKKNQIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY

Parental  LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKA
          LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKA
Retrocopy LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKA

Parental  EAGAGSATEFQFRGGFGRGRGQPPQ
          EAGAGSATEFQFRGGFGRGRGQPPQ
Retrocopy EAGAGSATEFQFRGGFGRGRGQPPQ

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	0.04 RPM	176.65 RPM
SRP017611_brain	0.00 RPM	49.14 RPM
SRP017611_kidney	0.40 RPM	282.51 RPM
SRP017611_liver	0.00 RPM	59.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 126 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408, retro_amel_1706, retro_amel_446, retro_amel_890,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1 , retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Cavia porcellus	ENSCPOG00000008613	2 retrocopies	retro_cpor_1245, retro_cpor_345,
Dasypus novemcinctus	ENSDNOG00000011670	2 retrocopies	retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii	ENSDORG00000012060	6 retrocopies	retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Nomascus leucogenys	ENSNLEG00000008336	24 retrocopies	retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Ochotona princeps	ENSOPRG00000002693	2 retrocopies	retro_opri_297, retro_opri_800,
Procavia capensis	ENSPCAG00000012795	1 retrocopy	retro_pcap_309,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Pan troglodytes	ENSPTRG00000018063	26 retrocopies	retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Tupaia belangeri	ENSTBEG00000001492	16 retrocopies	retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus	ENSTTRG00000015064	2 retrocopies	retro_ttru_1089, retro_ttru_1211,