RetrogeneDB ID: retro_fcat_678

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:200350811..200351277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000028951
• Aliases: None
• Description: None

Sequence

>retro_fcat_678
GAGATGACAGACAAACAGTCTCTGCATTTAGTAGAAAACAAAATCTAAGCAAACACAGACCAGATATTCAGCCATCTAGA
ACTTCTAGGGATTATGTCCAGCAAAGAGCCCCCTAACCAAAGAAAGAACGCCATGCTTCACACGGACAGGTTAAAGTAGC
ACACCCAGTACCTGTAGACTGCCCTCAGAAACTTCCAGCATCAGCGGTACACAAGGGCGCGGCAGAAGAAACAAGACAGC
AAGAGGAGCTGCTGCGTGCCACCTCCACCACTAATGACTCGACACCACCACCCTAATGCATGACTCACTGTGGTCTGACT
CTTCCCTCCAGAAAATTCACCATGGCATGGATGGCCTCAGTGGAGTCAGACACAGTATTCTGGAAGGACTGAGGGCCCAG
AGACTGACCTTGAAGGGGACTCAGAAGATCCCGGACACTGCCAACATGCTGGGCTTATCCAATAGT

Alignment

ORF - retro_fcat_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.55 %
• Parental protein coverage: 73.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETADKQSLHLVENEIQASIDQIFSHLERLEILSSKEPPNKRQNAKLRVDQLKYDVQHLQTALRNFQHRRY
          E..DKQSLHLVEN.I.A..DQIFSHLE.L.I.SSKEPPN.R.NA.L..D.LK...Q.L.TALRNFQH.RY
Retrocopy EMTDKQSLHLVENKI*ANTDQIFSHLELLGIMSSKEPPNQRKNAMLHTDRLK*HTQYL*TALRNFQHQRY

Parental  --AREQQE-RQREELLSRTFTANDS-DTTIPMDSSLHFNSSLQKIHHGMDDLIGGGHSILDGLRAQRLTL
          ..AR.....RQ.EELL..T.T.NDS.DTT..M..SL...SSLQKIHHGMD.L.G..HSIL.GLRAQRLTL
Retrocopy TRARQKKQ<RQQEELLRATSTTNDS<DTTTLMHDSLWSDSSLQKIHHGMDGLSGVRHSILEGLRAQRLTL

Parental  KGTQKKILDIANMLGLSNT
          KGTQK.I.D.ANMLGLSN.
Retrocopy KGTQK-IPDTANMLGLSNS

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	0.11 RPM	60.71 RPM
SRP017611_kidney	0.00 RPM	59.36 RPM
SRP017611_liver	0.00 RPM	44.78 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_678 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_678 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013419	1 retrocopy	retro_cfam_1351,
Callithrix jacchus	ENSCJAG00000020030	1 retrocopy	retro_cjac_3180,
Felis catus	ENSFCAG00000028951	1 retrocopy	retro_fcat_678 ,
Myotis lucifugus	ENSMLUG00000002709	1 retrocopy	retro_mluc_752,
Macaca mulatta	ENSMMUG00000018689	1 retrocopy	retro_mmul_367,
Nomascus leucogenys	ENSNLEG00000004922	1 retrocopy	retro_nleu_1211,
Pongo abelii	ENSPPYG00000008290	1 retrocopy	retro_pabe_1596,
Pan troglodytes	ENSPTRG00000009323	1 retrocopy	retro_ptro_1290,
Ictidomys tridecemlineatus	ENSSTOG00000016069	2 retrocopies	retro_itri_1790, retro_itri_270,