RetrogeneDB ID: retro_cfam_1396

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:91433934..91434308(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBY1
• Ensembl ID: ENSCAFG00000001384
• Aliases: None
• Description: chibby homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:1307]

Sequence

>retro_cfam_1396
CTCTTTGGGAATACGCTCGGTCCTAAGAAAACGCCCCCTCGGAAGTCTGCTTCTCTCTCCAACCCGCATGATCTGGATCG
ATCAACCAGGGAGGTCGCGCTGGGCCTGGGCTATGGAACCCCCACCATGAACCTGGTGGGACAAAGCCTGAAGTTTGAAA
ATGGCCAGCGAATCGCAGAGACGGGGATTAGCGGAGGTGTGGACCGGAGGGAGGCGAGCGGCTCCGCAGGCGGAACCAGC
AGTTGGAGGAAGCAAACAATCTCTTGAGGCTAAAGGTGGACGTCCTGCGGGACATGCTGTCTGAGACCGCTGCTGAGTCC
CGCTTGATGGAGAAGGAATTGGAGGAGCTGAAGAGCATCAGCCGCAGGAGGAAG

Alignment

ORF - retro_cfam_1396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFGNTFSPKKTPPRKSASLSNLHNLDRSTREVELGLDYGTPTMNLAGQSLKFENGQWIAETGISEDVDRR
          LFGNT..PKKTPPRKSASLSN.H.LDRSTREV.LGL.YGTPTMNL.GQSLKFENGQ.IAETGIS..VDRR
Retrocopy LFGNTLGPKKTPPRKSASLSNPHDLDRSTREVALGLGYGTPTMNLVGQSLKFENGQRIAETGISGGVDRR

Parental  EA-QRLRRRNQQLEEENNLLRLKVDILLDMLSETTAESHLMEKELEELKSISHRRK
          EA..RLRRRNQQLEE.NNLLRLKVD.L.DMLSET.AES.LMEKELEELKSIS.RRK
Retrocopy EA<ERLRRRNQQLEEANNLLRLKVDVLRDMLSETAAESRLMEKELEELKSISRRRK

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	6.17 RPM
SRP017611_brain	0.00 RPM	4.84 RPM
SRP017611_kidney	0.00 RPM	10.43 RPM
SRP017611_liver	0.07 RPM	2.39 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1396 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001384	2 retrocopies	retro_cfam_1396 , retro_cfam_852,
Dasypus novemcinctus	ENSDNOG00000010982	1 retrocopy	retro_dnov_875,
Homo sapiens	ENSG00000100211	1 retrocopy	retro_hsap_2344,
Gorilla gorilla	ENSGGOG00000013226	1 retrocopy	retro_ggor_1781,
Myotis lucifugus	ENSMLUG00000003757	2 retrocopies	retro_mluc_1128, retro_mluc_2608,
Mustela putorius furo	ENSMPUG00000013150	1 retrocopy	retro_mputfur_1186,
Nomascus leucogenys	ENSNLEG00000015153	1 retrocopy	retro_nleu_349,
Otolemur garnettii	ENSOGAG00000028533	1 retrocopy	retro_ogar_1072,
Pan troglodytes	ENSPTRG00000014373	1 retrocopy	retro_ptro_1716,
Vicugna pacos	ENSVPAG00000001484	1 retrocopy	retro_vpac_57,