RetrogeneDB ID: retro_fcat_1310

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:142557479..142557921(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSFCAG00000004448
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 9 [Source:HGNC Symbol;Acc:19123]

Sequence

>retro_fcat_1310
GAAGACTTTCAAGAGTTTGCAAAGATATGCCAAGGATCTGAGGAAGAGCTGGCCGATATTGAACAAGCCCGGCTGAACTT
CGAGAGGAACATGGGGCAGCCCACAGAATCTGTGCTGCATACGCGGCCCACTGAGTAACCCAGGATACGAAACGTCGTTC
AGCAAACCAATCACACCGGAGAGGGCCCAGCCTATGATGCTTTTGCCAAAGAATCAAAGCAAAAGATGAACGCAAGGAAA
AGGTCAGGGAAGAGGCTAAAGACCCAGAAATGACCTGGAAGGGGCTGGGGGCTTGATGAAGACACAGGTGGATACCCTGG
ATCCAGTTGTTCAAAGCAGGCAAAAGGACGGGCAACAGGAAATGGACACTGTTCTGACTCAGATGGAATCGAAGTATTAC
AAACCTTCCAAAAGCAGGAGTAAAGAGCTTTCAAGAAAGAAA

Alignment

ORF - retro_fcat_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.68 %
• Parental protein coverage: 56.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDIQAFEKTYKGSEEELADIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEIPSYNAFVK
          ED.Q.F.K...GSEEELADI.QA.L.F...M.Q..ESVL....TE.PRIRN..QQ....GE.P.Y.AF.K
Retrocopy EDFQEFAKICQGSEEELADIEQARLNFERNMGQPTESVLHTRPTE*PRIRNVVQQTNHTGEGPAYDAFAK

Parental  ESKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDNLKAVIQSRQ-KDR-QKEMDNFLAQMEAKYCKPSKR
          ESKQKMNARKR......K.........GLDE..........S.Q.K.R.Q.EMD..L.QME.KY.KPSK.
Retrocopy ESKQKMNARKR-SGKRLKTQK*PGRGWGLDEDTGGYPGSSCSKQAKGR>QQEMDTVLTQMESKYYKPSKS

Parental  GGKKTPLKK
          ..K....KK
Retrocopy RSKELSRKK

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	0.00 RPM	3.67 RPM
SRP017611_kidney	0.00 RPM	2.27 RPM
SRP017611_liver	0.00 RPM	2.43 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1310 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1310 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016933	1 retrocopy	retro_amel_478,
Felis catus	ENSFCAG00000004448	1 retrocopy	retro_fcat_1310 ,
Homo sapiens	ENSG00000213551	2 retrocopies	retro_hsap_1358, retro_hsap_2448,
Gorilla gorilla	ENSGGOG00000015046	3 retrocopies	retro_ggor_1058, retro_ggor_1499, retro_ggor_1524,
Myotis lucifugus	ENSMLUG00000004539	3 retrocopies	retro_mluc_699, retro_mluc_700, retro_mluc_955,
Mustela putorius furo	ENSMPUG00000003792	1 retrocopy	retro_mputfur_727,
Nomascus leucogenys	ENSNLEG00000016595	1 retrocopy	retro_nleu_1394,
Otolemur garnettii	ENSOGAG00000003496	2 retrocopies	retro_ogar_1730, retro_ogar_1740,
Pongo abelii	ENSPPYG00000002343	2 retrocopies	retro_pabe_1126, retro_pabe_1799,
Pan troglodytes	ENSPTRG00000034219	2 retrocopies	retro_ptro_1414, retro_ptro_931,
Ictidomys tridecemlineatus	ENSSTOG00000028067	1 retrocopy	retro_itri_413,
Tarsius syrichta	ENSTSYG00000011504	1 retrocopy	retro_tsyr_39,