RetrogeneDB ID: retro_fcat_96

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E3:20155739..20156786(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000030021
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSFCAG00000003921
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_fcat_96
GAAGGCGGCCTCCCGGCCGGGGCGGAACCCAACCCAACCTTTCCAGCCCTGGGCATTGGGATGGACTCCTGCGTCATACC
CCTGAGGCACGGGGGCCTGTCACTGGTGCAGACCACGGACTTCTTTTACCCCCTAGTGGAAGATCCCTACATGATGGGGC
GCATAGCGTGTGCCAACGTGCTGAGTGACCTCTACGCCATGGGTATTACTGAATGTGACAACATGTTGATGTTACTCAGC
GTCAGCCAGAGTATGACTGAGGAGGAACGAGAAAAGATAACACCGCTCATGATCAAAGGCTTTCGCGACGCTGCTGAGGA
AGGAGGGACTGCAGTGACTGGTGGACAGACAGTAGTAAACCCTTGGATTATCGTCGGAGGGGTTGCCACTGTGGTATGTC
AGCCAAATGAATTCATCATGCCGGACAGTGCAGTTGTTGGGGATGTGCTCGTGTTAACCAAACCCTTAGGAACCCAAGTT
GCTGTCAATGCCCACCAATGGCTGGATAATCCTGAAAGATGGAATAAAATAAATATGGTGGTCTCCAGAGAAGAGGTAGA
GCTAGCTTATCAGGAAGCCATGTTCAATATGGCTACCCTAAACAGAACTGCTGCTGGACTAATGCACACGTTTAATGCAC
ACGCAGCCACAGATATCACAGGCTTTGGCATTCTAGGACACTCTCAGAACCTTGCAAAACAACAAAGAAATGAGGTGTCA
TTTGTCATTCATAATCTGCCAATCATTGCCAAGATGGCTGCCATCAGCAAGGCCAGTGGGCGCTTTGGGCTCCTTCAAGG
AACCTCAGCAGAAACTTCTGGGGGATTACTGATTTGTCTGCCGAGAGAACAGGCAGCTCGCTTTTGTTCTGAAATCAAAT
CTTCCAAGTATGGAGAGGGTCACCAAGCATGGATCGTCGGTATTGTGGAAAAGGGAAACCGGACAGCTCGGATCATTGAC
AAGCCTCGAGTTATTGAGGTCCTACCTCGCGGGGCCACTGCTACTGCTCTTGTTCCTGACAATTCCAATGCTGCCTCTGA
ACCTAGC

Alignment

ORF - retro_fcat_96 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 82.98 %
• 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  SPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQ
          S.KYGEGHQAWI.GIVEKGNRTARIIDKPR.IEV.P.
Retrocopy SSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPR

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
SRP017611_brain	26.86 RPM	39.83 RPM
SRP017611_kidney	102.03 RPM	27.41 RPM
SRP017611_liver	140.21 RPM	27.19 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_96 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_96 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96 ,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
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,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,