RetrogeneDB ID: retro_cfam_1863

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:74795384..74795726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSCAFG00000009096
• Aliases: None
• Description: latexin [Source:HGNC Symbol;Acc:13347]

Sequence

>retro_cfam_1863
TTTAGAAGGGACTCTCAGTCCATGAAGGAACTACTTGAAGCACAAAATATTCCAGACAGTTTTGGAAATGTATGTCCAGA
AACGAAGCCAGTTTGACACTTAGCCTGTGGTTATATAATACAGCAGAATTCTACGGAAAACACATGGTATAAAATGGTAA
AAATTCAAACTGTCAAGCAGGTGCAAAGAAATGCTGACTTCATTGAGTTAGACTACACCATTCTACTTCCTGACATTGCA
TCTCAAGAGATTATTCCTTGGCAAATGCAAGTTCTCTGGCATCCTCAATATGGTAATAAAGTCAAACATAACGGCCATCT
GCCAAAGGAAGCACAACCGGAA

Alignment

ORF - retro_cfam_1863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 52.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FYQRLKSMKEPLEAQNIPDGLGNVPPEMEPVRHLAWVACGYVIWQNSTENTWYKMAKIHRVKQVQRNDDF
          F.....SMKE.LEAQNIPD..GNV.PE..PV.HL...ACGY.I.QNSTENTWYKM.KI..VKQVQRN.DF
Retrocopy FRRDSQSMKELLEAQNIPDSFGNVCPETKPV*HL---ACGYIIQQNSTENTWYKMVKIQTVKQVQRNADF

Parental  IELDYTVLLHDIASQEIIPWQMQVLWHPQYGTKVKHNTRLPKEAQPE
          IELDYT.LL.DIASQEIIPWQMQVLWHPQYG.KVKHN..LPKEAQPE
Retrocopy IELDYTILLPDIASQEIIPWQMQVLWHPQYGNKVKHNGHLPKEAQPE

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	3.95 RPM
SRP017611_brain	0.00 RPM	4.53 RPM
SRP017611_kidney	0.00 RPM	16.44 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1863 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1863 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863 ,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,