RetrogeneDB ID: retro_ecab_77

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:19239885..19240878(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003276
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSECAG00000014281
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:RefSeq peptide;Acc:NP_001177348]

Sequence

>retro_ecab_77
ATGGACTCCTGCGTCATACCCCTGAGGCACGGGGGCCTGTCACTGGTGCAGACCACGGACTTCTTTTACCCCTTGGTGGA
AGATCCTTACATGATGGGGCGCATAGCTTGCGCCAACGTGCTGAGTGACCTCTACGCCATGGGCATTACTGAATGTGACA
ACATGCTGATGTTGCTCAGCGTCAGCCAGAGTATGACTGAGGAGGAAAGAGAAAAGATAACACCACTGATGATCAGAGGC
TTTCGGGACGCTGCCGAGGAAGGAGGGACTGCAGTGACTGGGGGACAGACTGTGGTAAACCCCTGGATTATCGTCGGTGG
AGTTGCCACTGTGGTATGTCAGCCAAATGAATTTATAATGCCTGACAGTGCGGTTGTTGGGGATGTGCTCGTGTTAACCA
AACCCTTAGGAACCCAGGTTGCTGTGAATGCCCACCAATGGCTGGATAACCCTGAAAGATGGAATAAGATAAAGATGGTG
GTCTCCAGGGAAGAGGTAGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGCTACCCTAAACAGAACTGCTGCTGGATT
AATGCACACGTTTAATGCCCATGCAGCCACAGATATCACAGGCTTTGGCATTCTAGGACATTCCCAGAACCTTGCAAAAC
AACAAAGAAATGAGGTGTCCTTTGTCATACATAATCTGCCAATCATTGCCAAGATGGCTGCCATCAGCAAGGCCAGTGGA
CGCTTTGGGCTCCTTCAAGGAACCTCAGCAGAAACTTCCGGGGGGTTACTGATTTGTCTGCCAAGAGAACAGGCAGCTCG
CTTTTGTTCTGAAATCAAATCTTCCAAGTATGGAGAGGGTCACCAAGCATGGATCGTTGGCATTGTGGAAAAGGGAAACC
GGACGGCCCGGATCATTGACAAGCCTCGGGTTATTGAGGTCCTACCTCGTGGGGCCACTGCTACTGCTCTTGCTCCTGAC
AGTTCCAATGCCTCTTCTGAGCCTAGCTCTTGA

Alignment

ORF - retro_ecab_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 80.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRER
          MD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL.VS..MT..ER
Retrocopy MDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMTEEER

Parental  DKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQV
          .K..PL.I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTKPLGTQV
Retrocopy EKITPLMIRGFRDAAEEGGTAVTGGQTVVNPWIIVGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQV

Parental  AVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQN
          AV..HQWLD.PE.WNKIK.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGILGH.QN
Retrocopy AVNAHQWLDNPERWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQN

Parental  LAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGE
          LAKQQRNEVSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EIKS.KYGE
Retrocopy LAKQQRNEVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGE

Parental  GHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVAT
          GHQAWI.GIVEKGNRTARIIDKPR.IEV.P..AT
Retrocopy GHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGAT

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
SRP021940_articular_cartilage	16.76 RPM	31.70 RPM
SRP021940_cerebellum	33.24 RPM	48.56 RPM
SRP021940_embryo	17.67 RPM	72.32 RPM
SRP021940_placental_villous	20.11 RPM	15.83 RPM
SRP021940_synovial_membrane	16.44 RPM	31.05 RPM
SRP021940_testis	16.24 RPM	26.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_77 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_77 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_77 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77 ,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
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,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Ochotona princeps	ENSOPRG00000006587	3 retrocopies	retro_opri_271, retro_opri_655, retro_opri_670,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,