RetrogeneDB ID: retro_cfam_99

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:13156477..13157791(+)
• Located in intron of: ENSCAFG00000003169

Retrocopy information

• Ensembl ID: ENSCAFG00000015396
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSCAFG00000001282
• Aliases: None
• Description: None

Sequence

>retro_cfam_99
ATGGCGGACGACCCCAGTGCTGCCGACAGGAACGTGGAGATCTGGAAGATCAAGAAGCTCATCAAGAGCTTGGAGGCGGC
CCGCGGCAATGGCACAAGCATGATATCATTGATCATTCCTCCCAAAGACCAGATTTCACGAGTGGCAAAAATGTTAGCAG
ATGAGTTTGGAACTGCATCTAACATTAAGTCACGAGTAAACCGCCTTTCAGTCCTGGGAGCCATTACATCTGTACAACAA
AGACTCAAACTTTATAACAAAGTACCTCCAAATGGCCTGGTTGTTTACTGTGGTACAATTGTAACAGAAGAAGGAAAGGA
AAAGAAAGTCAACATTGACTTTGAACCTTTTAAACCAATTAATACGTCATTGTATTTGTGTGACAACAAATTCCATACAG
AGGCTCTTACAGCACTACTTTCAGATGACAGCAAGTTTGGCTTCATTGTAATAGATGGTAGTGGTGCACTTTTTGGCACA
CTCCAAGGAAACACAAGAGAAGTCTTGCACAAGTTCACTGTGGATCTCCCAAAGAAACATGGTAGAGGAGGTCAATCAGC
CTTGCGTTTTGCTCGTTTAAGAATGGAAAAGCGACATAACTATGTTCGGAAAGTAGCTGAGACTGCTGTACAGCTGTTTA
TTTCTGGGGACAAAGTGAATGTGGCTGGTCTTGTTTTAGCTGGATCAGCGGACTTTAAAACTGAACTAAGTCAATCTGAT
ATGTTTGATCAGAGGTTGCAATCAAAAGTTTTAAAATTAGTTGATATTTCCTATGGTGGCGAAAATGGATTCAACCAAGC
TATTGAGTTATCTACTGAAGTCCTTTCCAACGTGAAATTCATTCAAGAGAAGAAATTAATAGGACGATACTTTGATGAAA
TCAGCCAGGACACGGGCAAGTACTGTTTTGGAGTTGAAGATACACTAAAGGCTTTAGAAATGGGAGCTGTAGAGATTCTA
ATAGTCTATGAAAATCTGGATATAATGAGATATGTTCTTCATTGCCAAGGCACAGAAGAAGAGAAAATTCTCTATCTAAC
TCCAGAACAAGAGAAGGATAAATCTCATTTCACAGACAAAGAGACAGGACAAGAACATGAGCTGATTGAGAGTATGCCCC
TGCTGGAGTGGTTTGCTAACAATTATAAAAAATTTGGAGCTACATTGGAAATTGTCACAGATAAGTCACAAGAAGGATCC
CAGTTTGTGAAAGGATTTGGTGGAATTGGAGGTATCTTGCGGTACCGAGTAGATTTCCAGGGAATGGAATACCAAGGAGG
AGATGATGAATTTTTTGACCTTGATGACTACTAG

Alignment

ORF - retro_cfam_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLS
          MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLS
Retrocopy MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLS

Parental  VLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALL
          VLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALL
Retrocopy VLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALL

Parental  SDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAV
          SDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAV
Retrocopy SDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAV

Parental  QLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKF
          QLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKF
Retrocopy QLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKF

Parental  IQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQ
          IQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQ
Retrocopy IQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQ

Parental  EKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ
          EKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ
Retrocopy EKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ

Parental  GMEYQGGDDEFFDLDDY
          GMEYQGGDDEFFDLDDY
Retrocopy GMEYQGGDDEFFDLDDY

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	3.07 RPM	14.74 RPM
SRP017611_brain	2.54 RPM	12.94 RPM
SRP017611_kidney	3.24 RPM	17.50 RPM
SRP017611_liver	1.23 RPM	8.19 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_cfam_99 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DN342820	13156649	13156988	98.9	335	4	331
GR898023	13156726	13157275	100	549	0	549

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_99 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_99 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99 ,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,