RetrogeneDB ID: retro_cfam_1232

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:45131411..45131724(+)
• Located in intron of: ENSCAFG00000016136

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS15A
• Ensembl ID: ENSCAFG00000018174
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein S15a (RPS15A), mRNA. [Source:RefSeq mRNA;Acc:NM_001252147]

Sequence

>retro_cfam_1232
GTTCTTATTAGGACATGATTCAAAATCATTGTTCAGTTTCTCATTGTGATGATGAAGCATGGTTACATTGGCATATTTGA
AATCATTGATTATAGAGCTGGGTAAATTGTTGTGACGTCAGAGGCAGGTAAAACACGTGTGGAGTATCAGCCCCAGATTT
GATGTACAACTGAAAGATCTAGAAAAATGGCAGAGTAACCTGCTCCCGTCCTGCCAATTTGGTTTCATTGTCTTGAAAAC
CTCAACTAGCATCATGGACCATGAAGAAGCAAGAGAAAAACACACAGGAAGGGAAATCCCGAGATTCTTTTTT

Alignment

ORF - retro_cfam_1232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 81.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVV-NLTGRLNKCGV-ISPRFDVQLKDLEKWQNN
          VLIR...K.IV.FL.VMMKHGYIG.FEIID..RAG.IVV....GR.N.CGV.ISPRFDVQLKDLEKWQ.N
Retrocopy VLIRT*FKIIVQFLIVMMKHGYIGIFEIID-YRAG*IVV<DVRGR*NTCGV<ISPRFDVQLKDLEKWQSN

Parental  LLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF
          LLPS.QFGFIVL.TS..IMDHEEAR.KHTG..I..FFF
Retrocopy LLPSCQFGFIVLKTSTSIMDHEEAREKHTGREIPRFFF

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	130.57 RPM
SRP017611_brain	0.00 RPM	58.19 RPM
SRP017611_kidney	0.00 RPM	455.13 RPM
SRP017611_liver	0.00 RPM	125.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1232 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018174	20 retrocopies	retro_cfam_114, retro_cfam_1204, retro_cfam_1232 , retro_cfam_1261, retro_cfam_127, retro_cfam_1301, retro_cfam_1348, retro_cfam_1364, retro_cfam_1525, retro_cfam_1582, retro_cfam_1605, retro_cfam_1642, retro_cfam_1745, retro_cfam_1966, retro_cfam_21, retro_cfam_427, retro_cfam_464, retro_cfam_699, retro_cfam_831, retro_cfam_888,
Choloepus hoffmanni	ENSCHOG00000007800	5 retrocopies	retro_chof_1153, retro_chof_1320, retro_chof_2130, retro_chof_2284, retro_chof_270,
Callithrix jacchus	ENSCJAG00000020068	2 retrocopies	retro_cjac_782, retro_cjac_857,
Cavia porcellus	ENSCPOG00000012603	1 retrocopy	retro_cpor_291,
Erinaceus europaeus	ENSEEUG00000005434	1 retrocopy	retro_eeur_186,
Echinops telfairi	ENSETEG00000020152	2 retrocopies	retro_etel_2083, retro_etel_549,
Homo sapiens	ENSG00000170540	3 retrocopies	retro_hsap_1393, retro_hsap_559, retro_hsap_902,
Gorilla gorilla	ENSGGOG00000002902	3 retrocopies	retro_ggor_1080, retro_ggor_505, retro_ggor_729,
Loxodonta africana	ENSLAFG00000018632	2 retrocopies	retro_lafr_420, retro_lafr_741,
Macropus eugenii	ENSMEUG00000007896	1 retrocopy	retro_meug_1842,
Microcebus murinus	ENSMICG00000012246	5 retrocopies	retro_mmur_1383, retro_mmur_1561, retro_mmur_582, retro_mmur_939, retro_mmur_951,
Monodelphis domestica	ENSMODG00000005944	1 retrocopy	retro_mdom_794,
Nomascus leucogenys	ENSNLEG00000005499	2 retrocopies	retro_nleu_1079, retro_nleu_381,
Ornithorhynchus anatinus	ENSOANG00000012228	2 retrocopies	retro_oana_100, retro_oana_77,
Oryctolagus cuniculus	ENSOCUG00000005740	1 retrocopy	retro_ocun_1921,
Otolemur garnettii	ENSOGAG00000013202	2 retrocopies	retro_ogar_3502, retro_ogar_3504,
Pongo abelii	ENSPPYG00000007140	3 retrocopies	retro_pabe_1153, retro_pabe_2798, retro_pabe_777,
Pan troglodytes	ENSPTRG00000007824	3 retrocopies	retro_ptro_418, retro_ptro_622, retro_ptro_957,
Pteropus vampyrus	ENSPVAG00000002906	1 retrocopy	retro_pvam_1337,
Sarcophilus harrisii	ENSSHAG00000017346	1 retrocopy	retro_shar_691,
Ictidomys tridecemlineatus	ENSSTOG00000005816	1 retrocopy	retro_itri_1595,
Tupaia belangeri	ENSTBEG00000013916	3 retrocopies	retro_tbel_1609, retro_tbel_3046, retro_tbel_3772,
Tarsius syrichta	ENSTSYG00000011092	1 retrocopy	retro_tsyr_1528,
Tursiops truncatus	ENSTTRG00000005171	5 retrocopies	retro_ttru_1610, retro_ttru_1701, retro_ttru_519, retro_ttru_71, retro_ttru_929,