RetrogeneDB ID: retro_cfam_1087

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:52591337..52591718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSCAFG00000001336
• Aliases: None
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660]

Sequence

>retro_cfam_1087
GCTTCGTTAGTCCAGGCCACTGTCCGGGCTGTGAGCAAGGGGAAGCTGCAGCCCACCGGGGCCACCCTCACCCTGACCCC
TTCAGCAGTAAACAAGATAAAACAGCTACTTAAAGATAAGCCTGAACACGTAGGTCTCAAAGTTGGTGTCCGAACCAGGG
GTTGTAATGGCCTTTCCTATACTCTAGAATATACAAAGACAAAAGGAGATTCTGATGAAGAAGTTGTTCAAGATAGAGTC
AGAGTGTTCATCGAAAAGAAAGCACAGCTAACACTTTTAGGAACAGAAATGGACTATGTTGAAGATAAATTATCCAGTGA
GTTTATTTTCAATAACCCAAACATCAAAGGAACGTGTGGCTGTGGAGAAAGCTTTAATATT

Alignment

ORF - retro_cfam_1087 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.28 %
• Parental protein coverage: 71.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYTLEYTKTKGD
          ASLV.ATVRAVSK.KLQPT.A.LTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYTLEYTKTKGD
Retrocopy ASLVQATVRAVSKGKLQPTGATLTLTPSAVNKIKQLLKDKPEHVGLKVGVRTRGCNGLSYTLEYTKTKGD

Parental  SDEEVVQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFNI
          SDEEVVQD.VRVFIEKKAQLTLLGTEMDYVEDKLSSEF.FNNPNIKGTCGCGESFNI
Retrocopy SDEEVVQDRVRVFIEKKAQLTLLGTEMDYVEDKLSSEFIFNNPNIKGTCGCGESFNI

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	19.19 RPM
SRP017611_brain	0.08 RPM	16.04 RPM
SRP017611_kidney	0.26 RPM	58.51 RPM
SRP017611_liver	0.07 RPM	13.05 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1087 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Canis familiaris	ENSCAFG00000001336	1 retrocopy	retro_cfam_1087 ,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Equus caballus	ENSECAG00000011465	1 retrocopy	retro_ecab_936,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pteropus vampyrus	ENSPVAG00000004588	1 retrocopy	retro_pvam_956,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Sus scrofa	ENSSSCG00000010953	1 retrocopy	retro_sscr_558,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,
Tursiops truncatus	ENSTTRG00000004231	1 retrocopy	retro_ttru_1317,