RetrogeneDB ID: retro_fcat_1551

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D3:49906637..49907333(-)
• Located in intron of: ENSFCAG00000022853

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM178B
• Ensembl ID: ENSFCAG00000019142
• Aliases: None
• Description: family with sequence similarity 178, member B [Source:HGNC Symbol;Acc:28036]

Sequence

>retro_fcat_1551
GACCTCTTGGGCCTGATGGAGCCGCTGTGCTGAGTCAGCCTGGACGTGGGGCTCCACCTGCTGCCCAAGCCTGATCGCCA
TCAGTCTCTGCCTTCTGCTGGTCGAGAACTTCCAGGGGTGGCCAGGGAAGCTCCAGCAGCTGTGCTGCACCCCGAGCAAG
GTGTCAGAGTACTGCCACAATCTGCTGGTACTTGCATAGTTCTTTCTGACCTCCCAGACTAGGCAGCTTCAAAGCCAGCT
CAGCCTTGTGGTTGTTGCACAGATGCTGGACCAGCAAGAGACACTACTCCCTCTCTGGCAAGAGAAGGCCCAGCTGTCTT
TGCTCAGCCGGCTCCTGAGCCTCAGGAGGCCATCATCCCTCAGGCAGTACCTGGGCTCTGAGACCTTGCCACCGTGCCAG
GAGCAATAGCAAAAGGCCAGCACCAAACAAGACCATAATGTTTGCTCCCTGTGTCCCACTCTTCTGACACTCGCTGGGGT
GGTGGTCAGTTGCAGGACATTACTCCAGACCAATGGGGAGGGCTGCAGCAGCCATGCATGCAGTTGGACCGCCTCTCAGC
AACCATACCCGGGAGGGCCCCCAGGTCACGCACCCGACCAGACTCAAGGACCTAGCTGCCCAGACCGATATCTGCTGGAA
GGTGCTGCTGGCCCCACTGCTGGCCGCAGGCCCAGTACTTCAGCCCCTGGAAAGAC

Alignment

ORF - retro_fcat_1551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 54.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DLLGLIELLCRVGLDVGLRLLPKTDLQQ-LLLLLLENIHEWPRKLQKLCCSLSEVSDHHHNLLALVQFFL
          DLLGL.E.LC.V.LDVGL.LLPK.D..Q.L.LLL.EN...WP.KLQ.LCC..S.VS...HNLL.L..FFL
Retrocopy DLLGLMEPLC*VSLDVGLHLLPKPDRHQ>LCLLLVENFQGWPGKLQQLCCTPSKVSEYCHNLLVLA*FFL

Parental  DVTSRSRQLRSQLSLVVIARMLDQQETL-PLWQEKAQLSLLSQLLSLMRPSSLRQYLGSETLPPCQEQQP
          ..TS..RQL.SQLSLVV.A.MLDQQETL.PLWQEKAQLSLLS.LLSL.RPSSLRQYLGSETLPPCQEQ..
Retrocopy --TSQTRQLQSQLSLVVVAQMLDQQETLLPLWQEKAQLSLLSRLLSLRRPSSLRQYLGSETLPPCQEQ*Q

Parental  KTNAELDYKVCYLCHSLLTLAGVVVSC-QDITPDQWGELQLLCMQLDR-HINTHIRESPHAMHRTRLKDL
          K.....D..VC.LC..LLTLAGVVVSC.QDITPDQWG.LQ..CMQLDR.....H.RE.P...H.TRLKDL
Retrocopy KASTKQDHNVCSLCPTLLTLAGVVVSC<QDITPDQWGGLQQPCMQLDR<PLSNHTREGPQVTHPTRLKDL

Parental  AAQTYVRWQELLA-HCQPQAQYFSPWKD
          AAQT...W..LLA.HC.PQAQYFSPWKD
Retrocopy AAQTDICWKVLLA>HCWPQAQYFSPWKD

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	0.34 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1551 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1551 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000019142	1 retrocopy	retro_fcat_1551 ,
Mustela putorius furo	ENSMPUG00000011331	1 retrocopy	retro_mputfur_391,