RetrogeneDB ID: retro_cfam_1878

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:43030324..43030693(-)
• Located in intron of: ENSCAFG00000032170

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSCAFG00000009745
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_cfam_1878
CCTGCCCACGCTGCCCAGATGGCCTCCCGCAACTGCCACCCAGCGGCTGCCAACAAAGGTGCTGCCTGGGACCCTGTGGG
CAAGAGGCTGCATGAGGAGCTTATGTCCCTCACGGATGTCTGGCAACAAAGGAATTTCTGCCTTCCCTGAATCAGACCTT
TTCAAATGGGTGGGGACCATCACAGAACAGCTGGCAATGTGTAGGAGACTGAGGTCCAAGCTCTCCTTGGCGCTCCCAAG
GGGCTCCCCTTACAAGTCGCCCACAGTGAAGTTTTTCACGTCTGCTACCACCCCAATGTGGACACCCAGGGTCACACCTG
CCTGGACATCCTGCAGGACAGGTAATCTGCCGTGGGTGACATTAGGACC

Alignment

ORF - retro_cfam_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.69 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PAAASVAAARK--GAEPSGGAARGPVGKRLQQELMTLM-MSGDKGISAFPESDNLFKWVGTI-HGAAGTV
          PA.A...A.R....A....GAA..PVGKRL..ELM.L..MSG.KGISAFPESD.LFKWVGTI.H..AG.V
Retrocopy PAHAAQMASRNCHPAAANKGAAWDPVGKRLHEELMSLT>MSGNKGISAFPESD-LFKWVGTI<HRTAGNV

Parental  YEDLRYKLSLEFPSGY-PYNAPTVKFLTP-CYHPNVDTQGNICLDILKDKWSALYDVRT
          .E.......L..P.G..PY..PTVKF.T..CYHPNVDTQG..CLDIL.D..SA..D.RT
Retrocopy *E-TEVQALLGAPKGL>PYKSPTVKFFTS<CYHPNVDTQGHTCLDILQDR*SAVGDIRT

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	0.42 RPM	8.90 RPM
SRP017611_brain	0.32 RPM	0.08 RPM
SRP017611_kidney	0.13 RPM	0.40 RPM
SRP017611_liver	0.15 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1878 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016746	1 retrocopy	retro_btau_249,
Canis familiaris	ENSCAFG00000009745	6 retrocopies	retro_cfam_1031, retro_cfam_1805, retro_cfam_1878 , retro_cfam_2078, retro_cfam_290, retro_cfam_356,
Equus caballus	ENSECAG00000014619	2 retrocopies	retro_ecab_297, retro_ecab_316,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Felis catus	ENSFCAG00000001885	4 retrocopies	retro_fcat_1440, retro_fcat_1530, retro_fcat_1667, retro_fcat_1734,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Microcebus murinus	ENSMICG00000011218	2 retrocopies	retro_mmur_332, retro_mmur_988,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Sus scrofa	ENSSSCG00000007423	1 retrocopy	retro_sscr_643,