RetrogeneDB ID: retro_cfam_1955

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:39732282..39732755(-)
• Located in intron of: ENSCAFG00000016231

Retrocopy information

• Ensembl ID: ENSCAFG00000016250
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000003631
• Aliases: None
• Description: 40S ribosomal protein S11 [Source:UniProtKB/TrEMBL;Acc:F2Z4N5]

Sequence

>retro_cfam_1955
ATGGCAGACATTCAGACCAAGCGTGCCTACCAAAAGCAGCCAACCATCTTTCAAAATAAGAAGAGGTTCCTGCTTGGAGA
AACTGGCAAGGAGAAGCTCCCGCAGTACTACAAAAACATCGGTCTGGGCTTCAAGACGCCCAAGGAGGCCATTGAGGGCA
CCTATATTGACAAGAAATACCCCTTTACTGGCAATGTCTCCATCCAAGGGCAGATTTTGTCTGGTGTGGTGACCAAAATG
AAGATGCAGAGGACTATTGTCATCCGCCAAGACTCCTCCACTACATCCGAAAGTACAACTGCTTTGAGAAACGCCACAAG
AACATGTCGGTGCACTTGTCTCCTTGCTTCAGGGATGTCCAGATTGGCAACATTGTCACAATGGGTGAGTGCCGGCCCTG
GAGCAAGACTGTGCATTTCAACATGCTCAAAGTCACAAAAGCTGCTGGCACAAAGAAGCAGTTCCAGAAGTTC

Alignment

ORF - retro_cfam_1955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRG
          MADIQT.RAYQKQPTIFQNKKR.LLGETGKEKLP.YYKNIGLGFKTPKEAIEGTYIDKK.PFTGNVSI.G
Retrocopy MADIQTKRAYQKQPTIFQNKKRFLLGETGKEKLPQYYKNIGLGFKTPKEAIEGTYIDKKYPFTGNVSIQG

Parental  RILSGVVTKMKMQRTIVIRRD-YLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVR
          .ILSGVVTKMKMQRTIVIR.D..LHYIRKYN.FEKRHKNMSVHLSPCFRDVQIG.IVT.GECRP.SKTV.
Retrocopy QILSGVVTKMKMQRTIVIRQD<LLHYIRKYNCFEKRHKNMSVHLSPCFRDVQIGNIVTMGECRPWSKTVH

Parental  FNVLKVTKAAGTKKQFQKF
          FN.LKVTKAAGTKKQFQKF
Retrocopy FNMLKVTKAAGTKKQFQKF

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	0.08 RPM	395.92 RPM
SRP017611_brain	0.00 RPM	151.64 RPM
SRP017611_kidney	0.26 RPM	1110.55 RPM
SRP017611_liver	0.00 RPM	225.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1955 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1955 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 176 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014020	13 retrocopies	retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus	ENSBTAG00000013924	5 retrocopies	retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955 , retro_cfam_2121, retro_cfam_248,
Callithrix jacchus	ENSCJAG00000000069	1 retrocopy	retro_cjac_340,
Cavia porcellus	ENSCPOG00000015145	1 retrocopy	retro_cpor_534,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Dasypus novemcinctus	ENSDNOG00000016107	9 retrocopies	retro_dnov_1055, retro_dnov_1102, retro_dnov_1629, retro_dnov_1729, retro_dnov_188, retro_dnov_2520, retro_dnov_586, retro_dnov_68, retro_dnov_754,
Dipodomys ordii	ENSDORG00000012195	1 retrocopy	retro_dord_635,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Erinaceus europaeus	ENSEEUG00000003392	1 retrocopy	retro_eeur_75,
Felis catus	ENSFCAG00000009196	13 retrocopies	retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Homo sapiens	ENSG00000142534	6 retrocopies	retro_hsap_1017, retro_hsap_1068, retro_hsap_230, retro_hsap_2449, retro_hsap_4242, retro_hsap_4674,
Gorilla gorilla	ENSGGOG00000002936	6 retrocopies	retro_ggor_1525, retro_ggor_2843, retro_ggor_2900, retro_ggor_292, retro_ggor_805, retro_ggor_842,
Loxodonta africana	ENSLAFG00000016217	2 retrocopies	retro_lafr_622, retro_lafr_658,
Macropus eugenii	ENSMEUG00000008649	2 retrocopies	retro_meug_1176, retro_meug_1640,
Microcebus murinus	ENSMICG00000002542	8 retrocopies	retro_mmur_1278, retro_mmur_1317, retro_mmur_186, retro_mmur_295, retro_mmur_430, retro_mmur_452, retro_mmur_812, retro_mmur_820,
Myotis lucifugus	ENSMLUG00000030475	1 retrocopy	retro_mluc_539,
Macaca mulatta	ENSMMUG00000007549	6 retrocopies	retro_mmul_1147, retro_mmul_1856, retro_mmul_2464, retro_mmul_413, retro_mmul_634, retro_mmul_813,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Mustela putorius furo	ENSMPUG00000002599	10 retrocopies	retro_mputfur_1402, retro_mputfur_1507, retro_mputfur_200, retro_mputfur_306, retro_mputfur_345, retro_mputfur_485, retro_mputfur_491, retro_mputfur_626, retro_mputfur_781, retro_mputfur_897,
Mus musculus	ENSMUSG00000003429	16 retrocopies	retro_mmus_1738, retro_mmus_2230, retro_mmus_2255, retro_mmus_2322, retro_mmus_2486, retro_mmus_2854, retro_mmus_3048, retro_mmus_3051, retro_mmus_3060, retro_mmus_3342, retro_mmus_398, retro_mmus_404, retro_mmus_714, retro_mmus_754, retro_mmus_842, retro_mmus_860,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Procavia capensis	ENSPCAG00000004146	2 retrocopies	retro_pcap_333, retro_pcap_54,
Pongo abelii	ENSPPYG00000025860	5 retrocopies	retro_pabe_1800, retro_pabe_3396, retro_pabe_3631, retro_pabe_855, retro_pabe_889,
Pelodiscus sinensis	ENSPSIG00000011089	1 retrocopy	retro_psin_35,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus	ENSSARG00000003236	2 retrocopies	retro_sara_11, retro_sara_469,
Sarcophilus harrisii	ENSSHAG00000004991	1 retrocopy	retro_shar_649,
Sus scrofa	ENSSSCG00000003165	2 retrocopies	retro_sscr_432, retro_sscr_887,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,