RetrogeneDB ID: retro_cfam_1641

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:5466297..5466746(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A5
• Ensembl ID: ENSCAFG00000018384
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 [Source:HGNC Symbol;Acc:10991]

Sequence

>retro_cfam_1641
GTAGGCAAAGCTGGAGCCGAAAGGGAATTCAGAGACCGTGGTGACTGTCTGGCTAAGATCTACAAATCTGATGGGATTAA
GGGTCTGTGCCAAGGCTTTAATGTGTCTGTGCAGAGTATTATCATCTACCGAGCTATACTTTGGTATATATGACACTGCA
AAGGAATGCTTCCAGGTCCCAAGAATACTCATATCTTCATCAGTTGGATAATATTAGCAGTGATTCCTGGGTTGACTTCC
CATCAATTTGACATTGTTCATCACCATATGTTGATACAGTCAGGGTACAAAGTAACTGACGTCATGTACACAGGCAAGCT
TGACTACTAGAGGAAGATTGCTCATGATGAAGGAGCCAAAGCTTTTTTCAAGGGCACATATGCCAGTGTTCTCAGAGTCA
TGGTGGTGCTTTTATGCTTGTCTTGTCTGATGAAATCAAGAAGTTTACA

Alignment

ORF - retro_cfam_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.03 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGKAGAEREFRGLGDCLVKIYKSDGIRGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTHIFISW
          VGKAGAEREFR..GDCL.KIYKSDGI.GL.QGFNVSVQ.IIIYRA....I....KGMLP.PKNTHIFISW
Retrocopy VGKAGAEREFRDRGDCLAKIYKSDGIKGLCQGFNVSVQSIIIYRAILWYI*H-CKGMLPGPKNTHIFISW

Parental  MIAQSVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARDEGGKAFFKGAWSNVLRGM-G
          .I........GLTS..FD.V...M..QSG.K.TD.MYTG.LD..RKIA.DEG.KAFFKG....VLR.M.G
Retrocopy II---LAVIPGLTSHQFDIVHHHMLIQSGYKVTDVMYTGKLDY*RKIAHDEGAKAFFKGTYASVLRVM<G

Parental  GAFVLVLYDEIKKFT
          GAF.LVL.DEIKKFT
Retrocopy GAFMLVLSDEIKKFT

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	80.85 RPM
SRP017611_brain	0.16 RPM	74.07 RPM
SRP017611_kidney	0.00 RPM	306.54 RPM
SRP017611_liver	0.00 RPM	52.28 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1641 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018384	2 retrocopies	retro_cfam_1473, retro_cfam_1641 ,
Callithrix jacchus	ENSCJAG00000005125	1 retrocopy	retro_cjac_373,
Dasypus novemcinctus	ENSDNOG00000008384	1 retrocopy	retro_dnov_1894,
Echinops telfairi	ENSETEG00000004900	2 retrocopies	retro_etel_23, retro_etel_48,
Homo sapiens	ENSG00000005022	7 retrocopies	retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Gorilla gorilla	ENSGGOG00000014279	8 retrocopies	retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Loxodonta africana	ENSLAFG00000029398	1 retrocopy	retro_lafr_844,
Microcebus murinus	ENSMICG00000002757	3 retrocopies	retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus	ENSMLUG00000015742	4 retrocopies	retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta	ENSMMUG00000022663	6 retrocopies	retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys	ENSNLEG00000014852	7 retrocopies	retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105,
Oryctolagus cuniculus	ENSOCUG00000013268	11 retrocopies	retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pongo abelii	ENSPPYG00000020669	5 retrocopies	retro_pabe_1006, retro_pabe_2587, retro_pabe_3130, retro_pabe_3141, retro_pabe_3398,
Pteropus vampyrus	ENSPVAG00000014924	2 retrocopies	retro_pvam_1118, retro_pvam_911,
Rattus norvegicus	ENSRNOG00000039980	11 retrocopies	retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus	ENSSTOG00000020438	3 retrocopies	retro_itri_314, retro_itri_532, retro_itri_868,
Tupaia belangeri	ENSTBEG00000006008	4 retrocopies	retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,