RetrogeneDB ID: retro_cfam_1787

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:17668241..17669198(+)
• 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_1787
CCAGCCCTGGGCATCGGGATGGACTCCTGCGTCATCCCCCTGAGGCACGGGGGCCTGTCCCTGGTGCAGACCACGGACTT
CTTTTACCCCTTGGTGGAAGATCCCTACATGATGGGGCGCATAGCGTGTGCCAACGTGCTGAGTGACCTCTATGCCATGG
GCATTACTGAATGTGACAACATGTTGATGTTACTCAGCGTTAGCCAGAGTATGACTGAGGAGGAACGAGAGAAGATAACA
CCCCTTATGATCAAAGGCTTTCGCGACGCTGCTGAGGAAGGAGGGACTGCAGTGACTGGCGGACAGACAGTGGTAAACCC
TTGGATTATTGTCGGTGGGGTTGCCACTGTGGTATGTCAGCCAAATGAATTCATCATGCCTGACAGCGCCGTTGTTGGGG
ATGTGCTCGTGTTAACCAAACCCCTAGGAACCCAAGTTGCTGTTAATGCCCACCAATGGCTAGATAACCCTGAGAGATGG
AATAAAATAAATATGGTGGTCTCCAGGGAAGAGGTAGAGCTGGCTTATCAGGAAGCCATGTTCAATATGGCTACCCTGAA
CAGAACTGCTGCTGGATTAATGCACACGTTTAATGCACATGCAGCCACAGATATCACCGGTTTTGGCATTCTGGGACACT
CTCAGAACCTTGCAAAACAACAAAGAAACGAGGTGTCCTTTGTTATTCATAATCTGCCAATCATCGCCAAGATGGCTGCT
ATCAGCAAGGCCAGTGGGCGCTTTGGGCTCCTTCAAGGAACCTCAGCGGAAACTTCTGGTGGATTGCTGATTTGTCTGCC
AAGAGAACAGGCAGCTCGCTTTTGTTCTGAAATAAAATCTTCCAAGTATGGAGAGGGTCACCAGGCATGGATCGTCGGTA
TTGTGGAAAAGGGAAACCGGACAGCCCGGATTATTGACAAGCCTCGAGTTATTGAGGTCCTACCTCGTGGGGCCACT

Alignment

ORF - retro_cfam_1787 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 81.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNK
          P.LGIGMD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL..S..
Retrocopy PALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQS

Parental  MTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTK
          MT..ER.K..PL.I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTK
Retrocopy MTEEEREKITPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIVGGVATVVCQPNEFIMPDSAVVGDVLVLTK

Parental  PLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGI
          PLGTQVAV..HQWLD.PE.WNKI..VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGI
Retrocopy PLGTQVAVNAHQWLDNPERWNKINMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGI

Parental  LGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIK
          LGH.QNLAKQQRNEVSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EIK
Retrocopy LGHSQNLAKQQRNEVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIK

Parental  SPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVAT
          S.KYGEGHQAWI.GIVEKGNRTARIIDKPR.IEV.P..AT
Retrocopy SSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGAT

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	18.23 RPM	153.72 RPM
SRP017611_brain	16.91 RPM	59.86 RPM
SRP017611_kidney	130.16 RPM	93.24 RPM
SRP017611_liver	127.04 RPM	33.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1787 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1787 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,