RetrogeneDB ID: retro_cfam_898

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:42964466..42964835(+)
• Located in intron of: ENSCAFG00000006851

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7C
• Ensembl ID: ENSCAFG00000016715
• Aliases: None
• Description: B-cell CLL/lymphoma 7C [Source:HGNC Symbol;Acc:1006]

Sequence

>retro_cfam_898
GAAAACAGTAATCAGAGTTTCCATTCGGAAGGCTCCCTGCAAAAGGGCACCGAACCCAGCCCTGGGGGTACCCCCCAGCC
CAGCTGCCCTGTGTCACCTGCTGGACCACCAGAAGGGGTCCCAGAGGATGCTCAGCCCCCACAGCTGGGCCAAGAGAGAG
ATCCTGAGGGCATCACTGCAGGCAGCACCCATGAACCCCCAATGCTGACCAAGGAGGAGCCTGTTCCAGAATTGCTGGAG
GCTGAGGCCCCCGAAGCTTACCCCGTCTTTGAGCCAGTGCCACCTGTCCCCGATGCAGCCCAGGGTGACACAGAGGACTC
GGAGGGTGCCCCCCCACTCAAGCGCATCTGCCCAAATGCCCCTGACCCC

Alignment

ORF - retro_cfam_898 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.93 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENSNQSFHSEGSLQKGTEPSPGGTPQPSRPVSPAGPPEGVPEDAQPPRLGQERDPGGITAGSTDEPPMLT
          ENSNQSFHSEGSLQKGTEPSPGGTPQPS.PVSPAGPPEGVPEDAQPP.LGQERDP.GITAGST.EPPMLT
Retrocopy ENSNQSFHSEGSLQKGTEPSPGGTPQPSCPVSPAGPPEGVPEDAQPPQLGQERDPEGITAGSTHEPPMLT

Parental  KEEPVPELLEAEAPEAYPVFEPVPPVPEAAQGDTEDSEGAPPLKRICPNAPDP
          KEEPVPELLEAEAPEAYPVFEPVPPVP.AAQGDTEDSEGAPPLKRICPNAPDP
Retrocopy KEEPVPELLEAEAPEAYPVFEPVPPVPDAAQGDTEDSEGAPPLKRICPNAPDP

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	21.08 RPM
SRP017611_brain	0.00 RPM	4.37 RPM
SRP017611_kidney	0.00 RPM	7.26 RPM
SRP017611_liver	0.00 RPM	1.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_898 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_898 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898 ,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613, retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,