RetrogeneDB ID: retro_cfam_1285

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:1767668..1768185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18
• Ensembl ID: ENSCAFG00000003967
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein L18 (RPL18), mRNA. [Source:RefSeq mRNA;Acc:NM_001251958]

Sequence

>retro_cfam_1285
AAGGAGGAGCCCAAGAGCCAGGACATCTACCTGAGACTGTTGGTCAATTTGCACAGGTTTCTTTCCCCATTAGCCTACTC
TACCTTTAGCCAACTTGTGTTGAAGTGGTTGTTCATGAGTTGCACCAACCCACTTCCTCAGCCCCAATCCTGGATGATCC
AGAAGATGAAGCTGCCTGACTGGGAAAACAAAATAGCTGTTGCTGTAGGTACTATAACTTATGATGTGCATGCACAGGAG
GTGCCAAACTGAAGGTGTGTACACTGCGCCTGAATTGCCATGCCTGGAGTTACATCCTCAATGTTGGGGCAAGAGCCTCA
CCTTCAACCAGGTGGCCCTAGACTCTCTCAAGAACTGTGGTACTATCTTGGTCTCTGGTCCAGACAGGCCCTGAGAAGTA
TACAGGAATTTCAGTAAGGCCACAAGAACCCCATATAGCCACAACAAACTCCACTTGCAATCCAAGGGCTAGAAGTTCCA
GTGCCACAGAGGCTCCAGAGCCAGCCAGTACAAAAAC

Alignment

ORF - retro_cfam_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 92.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKMKLPGRENKTAVVVG
          ..EPKSQDIYLRLLV.L.RFL.....STF.Q.VLK.LFMS.TN..P...S.MI.KMKLP..ENK.AV.VG
Retrocopy KEEPKSQDIYLRLLVNLHRFLSPLAYSTFSQLVLKWLFMSCTNPLPQPQSWMIQKMKLPDWENKIAVAVG

Parental  TITDDVRVQEVP-KLKVCALRVSSRARSRILKAG-GKILTFDQLALDSPKGCGTVLLSGPRKGREVYRHF
          TIT.DV..QEVP.KLKVC.LR....A.S.IL..G.GK.LTF.Q.ALDS.K.CGT.L.SGP....EVYR.F
Retrocopy TITYDVHAQEVP<KLKVCTLRLNCHAWSYILNVG<GKSLTFNQVALDSLKNCGTILVSGPDRP*EVYRNF

Parental  GKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN
          .KA..TP.SH.K....SKG.KF...RG.RAS..YKN
Retrocopy SKATRTPYSHNKLHLQSKG*KFQCHRGSRASQ-YKN

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	188.66 RPM
SRP017611_brain	0.00 RPM	62.08 RPM
SRP017611_kidney	0.00 RPM	536.75 RPM
SRP017611_liver	0.00 RPM	161.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1285 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1285 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 155 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014872	3 retrocopies	retro_amel_1718, retro_amel_640, retro_amel_740,
Bos taurus	ENSBTAG00000015388	1 retrocopy	retro_btau_845,
Canis familiaris	ENSCAFG00000003967	7 retrocopies	retro_cfam_1285 , retro_cfam_1383, retro_cfam_1507, retro_cfam_1853, retro_cfam_2044, retro_cfam_2199, retro_cfam_304,
Choloepus hoffmanni	ENSCHOG00000009140	6 retrocopies	retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Equus caballus	ENSECAG00000021927	3 retrocopies	retro_ecab_478, retro_ecab_530, retro_ecab_880,
Erinaceus europaeus	ENSEEUG00000015872	5 retrocopies	retro_eeur_176, retro_eeur_299, retro_eeur_381, retro_eeur_419, retro_eeur_437,
Echinops telfairi	ENSETEG00000013157	6 retrocopies	retro_etel_1059, retro_etel_1211, retro_etel_1342, retro_etel_1373, retro_etel_1391, retro_etel_1715,
Felis catus	ENSFCAG00000008652	4 retrocopies	retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Gorilla gorilla	ENSGGOG00000024878	7 retrocopies	retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Loxodonta africana	ENSLAFG00000031267	1 retrocopy	retro_lafr_879,
Macropus eugenii	ENSMEUG00000000640	1 retrocopy	retro_meug_1568,
Myotis lucifugus	ENSMLUG00000009286	12 retrocopies	retro_mluc_1440, retro_mluc_1442, retro_mluc_1462, retro_mluc_1736, retro_mluc_1791, retro_mluc_1912, retro_mluc_2023, retro_mluc_480, retro_mluc_729, retro_mluc_786, retro_mluc_886, retro_mluc_904,
Macaca mulatta	ENSMMUG00000022158	3 retrocopies	retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica	ENSMODG00000014099	1 retrocopy	retro_mdom_906,
Mustela putorius furo	ENSMPUG00000003891	4 retrocopies	retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Nomascus leucogenys	ENSNLEG00000004537	11 retrocopies	retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii	ENSOGAG00000003562	16 retrocopies	retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus	ENSONIG00000006539	1 retrocopy	retro_onil_43,
Pongo abelii	ENSPPYG00000010206	6 retrocopies	retro_pabe_1003, retro_pabe_1337, retro_pabe_1402, retro_pabe_2681, retro_pabe_3100, retro_pabe_3176,
Pteropus vampyrus	ENSPVAG00000009524	10 retrocopies	retro_pvam_101, retro_pvam_1034, retro_pvam_1244, retro_pvam_1376, retro_pvam_1444, retro_pvam_427, retro_pvam_785, retro_pvam_883, retro_pvam_969, retro_pvam_990,
Rattus norvegicus	ENSRNOG00000021035	14 retrocopies	retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii	ENSSHAG00000006564	2 retrocopies	retro_shar_571, retro_shar_659,
Sus scrofa	ENSSSCG00000025928	5 retrocopies	retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus	ENSSTOG00000012258	5 retrocopies	retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,
Tupaia belangeri	ENSTBEG00000001594	18 retrocopies	retro_tbel_1006, retro_tbel_126, retro_tbel_1591, retro_tbel_1599, retro_tbel_1600, retro_tbel_1719, retro_tbel_2618, retro_tbel_2628, retro_tbel_277, retro_tbel_2984, retro_tbel_3527, retro_tbel_3529, retro_tbel_3608, retro_tbel_3609, retro_tbel_4409, retro_tbel_4473, retro_tbel_4590, retro_tbel_737,
Tursiops truncatus	ENSTTRG00000008187	3 retrocopies	retro_ttru_1127, retro_ttru_1770, retro_ttru_42,