RetrogeneDB ID: retro_cfam_1140

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:8997729..8998492(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005504
• Aliases: None
• Description: None

Sequence

>retro_cfam_1140
ATGGCCAGCAATGTTACCAACAAGACAGATCCTAGCTCCATGAACTCCCGTGTATTCATTGGGAATCTCAATACTCTTGT
GGTCAAGAAATCTTATGTGGAGGCAATCTTCTCAAAATATGGCAAAATTGTGGGTTGCTCTGTTCATAAAGGCTTTGCCT
TCATTCAGTATGTTAATGAGAGAAATGCCCAGGCTGCTGTGGCAGGAAAGGATGGCAGAATGATTGCTGGCCAGGTTTTA
GATATTAATCTGGCTGCAGAGTCAAAAGTAAACCAAGGAAAAGCAGGTGTGAAACGATCTGTAGTGGAGATGTACAGGTC
AGTACCAGAACACCCTTCTCCATCCCCTCTACTCAGCTCCTCTTTTGATTTGGACTATGACTTTCAACAAGATTATTATA
ACAGGATGTACAGTTTCCCAGCATGTGTTCCTCCTCCTCCTCCTCCAATTGCTTGTGCTGTGGTTCCCTCAAAATACCAG
CGTGTATCAGGAAACACCTCAGGAAGGGACAAACGTGGTTTCAATTCTAAGAGTGGACAGCAAGGATCTTCTTCCAAGTA
AGGAAAGTTGAAAGGAGATGACCTTCAGACCATTAAGAAGGAGTTGACCTAGATAAAACAAAAAGTGGATTCTTTACTGG
AAAGCCTGGAAAAAAACTGAGAAAGAACGGAGCAAACAAGGAGTAGAGATGAAGAATGATAAGTCAGAAGAGGAGCAGAA
CAGCAGCTCCCTGAAGAAAGATGAGACTAATGTGAAGATGGAG

Alignment

ORF - retro_cfam_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 75.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGE
          MASNVTNKTDP.SMNSRVFIGNLNTLVVKKS.VEAIFSKYGKIVGCSVHKGFAF.QYVNERNA.AAVAG.
Retrocopy MASNVTNKTDPSSMNSRVFIGNLNTLVVKKSYVEAIFSKYGKIVGCSVHKGFAFIQYVNERNAQAAVAGK

Parental  DGRMIAGQVLDINLAAEPKVNRGKAGVKRSAAEMYGSVPEHPSPSPLLSSSFDLDYDFQRDYYDRMYSYP
          DGRMIAGQVLDINLAAE.KVN.GKAGVKRS..EMY.SVPEHPSPSPLLSSSFDLDYDFQ.DYY.RMYS.P
Retrocopy DGRMIAGQVLDINLAAESKVNQGKAGVKRSVVEMYRSVPEHPSPSPLLSSSFDLDYDFQQDYYNRMYSFP

Parental  ARV-PPPPPIARAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSSKSGKLKGDDLQTIKKELTQIKQKVD
          A.V.PPPPPIA.AVVPSK.QRVSGNTS.R.K.GFNSKSGQ.GSSSK.GKLKGDDLQTIKKELT.IKQKVD
Retrocopy ACVPPPPPPIACAVVPSKYQRVSGNTSGRDKRGFNSKSGQQGSSSK*GKLKGDDLQTIKKELT*IKQKVD

Parental  SLLESLE-KIEKEQSKQTDLSFSSPVEMKNDKSEEEQSSSSLKKD
          SLLESLE.K.EKE.SKQ.........E.....S.........K..
Retrocopy SLLESLE>KTEKERSKQGVEMKNDKSEEEQNSSSLKKDETNVKME

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	0.34 RPM	97.61 RPM
SRP017611_brain	0.00 RPM	53.19 RPM
SRP017611_kidney	0.07 RPM	128.64 RPM
SRP017611_liver	0.00 RPM	32.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1140 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011396	2 retrocopies	retro_btau_1084, retro_btau_1142,
Canis familiaris	ENSCAFG00000005504	1 retrocopy	retro_cfam_1140 ,
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624, retro_hsap_3740,
Gorilla gorilla	ENSGGOG00000023015	1 retrocopy	retro_ggor_1046,
Microcebus murinus	ENSMICG00000007682	2 retrocopies	retro_mmur_1439, retro_mmur_863,
Macaca mulatta	ENSMMUG00000014809	4 retrocopies	retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furo	ENSMPUG00000000164	2 retrocopies	retro_mputfur_231, retro_mputfur_241,
Mus musculus	ENSMUSG00000060373	1 retrocopy	retro_mmus_1388,
Nomascus leucogenys	ENSNLEG00000014362	2 retrocopies	retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus	ENSOCUG00000015029	1 retrocopy	retro_ocun_138,
Otolemur garnettii	ENSOGAG00000012543	1 retrocopy	retro_ogar_165,
Pongo abelii	ENSPPYG00000005593	6 retrocopies	retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes	ENSPTRG00000006118	2 retrocopies	retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus	ENSRNOG00000011621	1 retrocopy	retro_rnor_922,
Tupaia belangeri	ENSTBEG00000011514	11 retrocopies	retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,
Tarsius syrichta	ENSTSYG00000003305	3 retrocopies	retro_tsyr_1004, retro_tsyr_1326, retro_tsyr_1411,
Tursiops truncatus	ENSTTRG00000016055	2 retrocopies	retro_ttru_1299, retro_ttru_1490,