RetrogeneDB ID: retro_cfam_250

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:25118210..25119156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSCAFG00000004743
• Aliases: None
• Description: Canis lupus familiaris selenophosphate synthetase 1 (SEPHS1), mRNA. [Source:RefSeq mRNA;Acc:NM_001190410]

Sequence

>retro_cfam_250
GGTGGTCTTTCTTTGGTTCAAACCACGGATTACATTTACCCCATTGTTGATGACCCTTACATGATGGGCAGGATAGCATG
TGCCAACGTCCTCAGTGACCTCTACGCCATGGGGGTCACGGAATGTGACAATATGCTGATGCTCCTTGGGATCAGTAATA
AAATGACTGACAGGGAGAAGGGATAAAGTGATGCCCCTAATTATACAGGGTTTTAAAGATGCAGCAGAGGAGGTGGGAAC
GTCTGTGACTGGTGGCCAAACGGTGTTAAACCCCTGGATTGTTCTAGGAGGAGTGGCTACTACTATCTGCCAGCCCAATG
AATTCATCATGCCAGATAACACAATCCCGGGGGATGTGCTGGTGATGACGAAGCCCCTGGGGATGCAGGTGGCTGTGGCT
GTGCACCAGTGGCTGGACATTCCTGAAAAATGGAATAAGATCAAGCTAGTGGTCACCCAAGAAGATGTAGAGTTGGCGTA
CCAGGAGCCGATGATGAACATGGCCAGGCTCAACAGAACAGCTGCGGGACTCATGCACACGTTCAATGCCCACACCGCCA
CTGACATCACGGGCTTTGGGATTTTGGGGCACGCGCAGAACCTAGCCAAGCAGCAGAGGAACGAGGTGTCCTTCATGATT
CACAACCTCCCTGTCCTGGCCAAGATGGCTGTTGTGAGCAAGGCCTGTGGAAACATGTTTGGCCTCATGCATGGGACCTG
CCCAGAGACATCAGGAGGCCTCCTCATCTGTTTACCGTGAGAGCAAGCCTCCCGGTTCTGTGCAGAGATCAAGTCTCCCA
AATATGGGGAGGGCCACCAGGCATGGATTATTGGGATCGTGGAGAAAGGCAACCGCACCGCCAGAATCATAGACAAGCCC
CGGATCATCGAAGTTGCACCACAGGTGGCCACTCAGAAAGTGAACCCCACCCCGGGTGCCACCTCT

Alignment

ORF - retro_cfam_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.57 %
• Parental protein coverage: 80.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDRE-RDKVMPLIIQ
          GGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDRE.RDKVMPLIIQ
Retrocopy GGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDRE>RDKVMPLIIQ

Parental  GFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLD
          GFKDAAEE.GTSVTGGQTVLNPWIVLGGVATT.CQPNEFIMPDN..PGDVLV.TKPLG.QVAVAVHQWLD
Retrocopy GFKDAAEEVGTSVTGGQTVLNPWIVLGGVATTICQPNEFIMPDNTIPGDVLVMTKPLGMQVAVAVHQWLD

Parental  IPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEV
          IPEKWNKIKLVVTQEDVELAYQE.MMNMARLNRTAAGLMHTFNAH.ATDITGFGILGHAQNLAKQQRNEV
Retrocopy IPEKWNKIKLVVTQEDVELAYQEPMMNMARLNRTAAGLMHTFNAHTATDITGFGILGHAQNLAKQQRNEV

Parental  SFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGI
          SF.IHNLPVLAKMA.VSKACGNMFGLMHGTCPETSGGLLICLP.EQA.RFCAEIKSPKYGEGHQAWIIGI
Retrocopy SFMIHNLPVLAKMAVVSKACGNMFGLMHGTCPETSGGLLICLP*EQASRFCAEIKSPKYGEGHQAWIIGI

Parental  VEKGNRTARIIDKPRIIEVAPQVATQNVNPTPGATS
          VEKGNRTARIIDKPRIIEVAPQVATQ.VNPTPGATS
Retrocopy VEKGNRTARIIDKPRIIEVAPQVATQKVNPTPGATS

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	153.72 RPM
SRP017611_brain	0.00 RPM	59.86 RPM
SRP017611_kidney	0.07 RPM	93.24 RPM
SRP017611_liver	0.15 RPM	33.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_250 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250 ,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,