RetrogeneDB ID: retro_cfam_471

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:60739033..60739515(-)
• Located in intron of: ENSCAFG00000023949

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG4
• Ensembl ID: ENSCAFG00000014210
• Aliases: None
• Description: B-cell translocation gene 4 [Source:HGNC Symbol;Acc:13862]

Sequence

>retro_cfam_471
TGCCCTTCCAAAGGGCAAGCCTTCAGGTGTATCAGGATAAATAATAATCAATAAAGATCCCATTCTAGAAAGGGTTTGTG
CTGAAAGTAACATGGATTTTTCTCACCTGGGACTTCCAAAGGAGATGACCGTATGGGTAGATCCCTTTGAAGTGTGGTGT
AGGTATGGTGAGAAAAATCATCCATTTACAATTGCTTCTTTTAAAAGGCAGGGGGGAGGAATGGGAGCTTACCCAGCAGA
TCAGCTTTGCTGTTAATAGAGCCACTTTAGACCACACCTCAGGCATTTCCTCTGTTGAAGAAAGTTGTAACAAAGAACCT
CAGATCATTCCTAAAGTCAGTAATCCGAAGAGTATATATCAGGTTGAAAACTTAAAACAGCCCTTTCAATCTTGGTTCCA
TGTCTCCCACAAAAAGAATATGACACATGGCCATATGGGCCTCCTAGGGAACACTTCTCATGCATTGCATAAACATCCTA
AA

Alignment

ORF - retro_cfam_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 64.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CPSKGQAFRCIRINNNQ-NKDPILERACAESNVDFSHLGLPKEMTLWVDPFEVCCRYGEKNHPFTIASFK
          CPSKGQAFRCIRI.NN..NKDPILER.CAESN.DFSHLGLPKEMT.WVDPFEV.CRYGEKNHPFTIASFK
Retrocopy CPSKGQAFRCIRI-NNN>NKDPILERVCAESNMDFSHLGLPKEMTVWVDPFEVWCRYGEKNHPFTIASFK

Parental  -GRWEEWELTQQISFAVNRATLDSTSGISSDEESSNKEPQIIPKVSNPKSIYQVENLKPPFQSWFHVSRK
          .GR.EEWELTQQISFAVNRATLD.TSGISS.EES.NKEPQIIPKVSNPKSIYQVENLK.PFQSWFHVS.K
Retrocopy >GRGEEWELTQQISFAVNRATLDHTSGISSVEESCNKEPQIIPKVSNPKSIYQVENLKQPFQSWFHVSHK

Parental  KNMADGRMGLLGNTSHASHKHPK
          KNM..G.MGLLGNTSHA.HKHPK
Retrocopy KNMTHGHMGLLGNTSHALHKHPK

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	0.25 RPM	0.17 RPM
SRP017611_brain	0.16 RPM	0.24 RPM
SRP017611_kidney	0.07 RPM	0.00 RPM
SRP017611_liver	0.07 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_471 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_471 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014210	2 retrocopies	retro_cfam_1324, retro_cfam_471 ,
Choloepus hoffmanni	ENSCHOG00000000032	1 retrocopy	retro_chof_2674,
Equus caballus	ENSECAG00000012564	1 retrocopy	retro_ecab_299,
Monodelphis domestica	ENSMODG00000014496	1 retrocopy	retro_mdom_1647,
Sus scrofa	ENSSSCG00000015020	1 retrocopy	retro_sscr_680,
Tursiops truncatus	ENSTTRG00000010435	1 retrocopy	retro_ttru_1303,