RetrogeneDB ID: retro_fcat_1179

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:46023818..46024812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FARSB
• Ensembl ID: ENSFCAG00000026772
• Aliases: None
• Description: phenylalanyl-tRNA synthetase, beta subunit [Source:HGNC Symbol;Acc:17800]

Sequence

>retro_fcat_1179
TTTATATATATCTTTGGAAATAAACCACTATACCCAGTTGTCCATGATAGCAATGGTGCTGTCATTTTAAGGCCTATCAT
CAATGAAAATAACTCCAAATTAACAGTAAATACTAGAATGGATTCCCTGGATGCACAGGAACTGACTTTACTAAGGCAAA
AATAGTTCTTGCTGTCATTGTCACCATGTTCAGTGAATATTATGAGAATCAATTCACGATTGAATCAGCTGAGGTGGTTT
TTCCTAATGGAAAATCACATACCATTCCAGAACTGACTTAATGAAAGGAGGTGGTGATATCTGATCCAATTAACAAATAA
GTTGGAACCAGAGCAATTCCAGAAAATTTTGCGAAACTTCTGACTAGGATGGATTTAAAGTCAGAAGTCATAGGTTATGG
GAATTGAATTGAGATTGAAATCTCTCCAACCAGAGCTGACATTATCCATGCATGTGATATTGTAAAAGATGGAGCTATTG
CTTATGGATATAGCAACATTCAGGTGGCTCTCCCAGAAACATACACTGTAACTAATCAGTTTCCTCTTAACAAGCTCAGA
GGACTTCTAAGACATGACAGGGTAGCTGCTGGATTCACTGAAGACTCGGCTTTCGTCTGTGCCCCCAAGGAGGTGTTGCT
GATAAACTTGGTTTCGACATCTCTGCAACAAAGGCAGTTCATATAAGTGATTCTACAGCCATTTAATTTCAGATGGTACA
CATTGCCCTTCTTCCTGGCCTCCTAAAGACCATAGCCACAAATTATATGATGCCCCTTCCTCTAAAACAAATCTCTGACA
CTGTAGTAAAAAATGCTAGCAGAGACGTAGGTGAAAGGAACTACAGGCATCTCTGTGCTATTTATTACAGTAAGAATCCT
TGGTTTGAAACAATCCGTGGGTTTCTGGACAGAATTATACAGCTGCTTCATGTGCCTCCTGGTGAAAAGAAGGGGGATGG
CGTGATCACAGCATCAGAAGGCCCTTCCTTCTGG

Alignment

ORF - retro_fcat_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.73 %
• Parental protein coverage: 56.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YLHIIENKPLFPVIYDSNGVVLSMPPIINGNHSKITVNTR-NVFIECTGTDFTKAKIVLDVIVTMFSEYC
          ...I..NKPL.PV..DSNG.V....PIIN.N.SK.TVNTR.N.F..CTGTDFTKAKIVL.VIVTMFSEY.
Retrocopy FIYIFGNKPLYPVVHDSNGAVI-LRPIINENNSKLTVNTR<NGFPGCTGTDFTKAKIVLAVIVTMFSEYY

Parental  ENPFMVEAAEVVFPNGKSYIFPELAYRKEIVRADLINKKVGIRETPENIAKLLTRMHLKSEVIGDGNQIE
          EN.F..E.AEVVFPNGKS...PEL...KE.V..D.INK.VG.R..PEN.AKLLTRM.LKSEVIG.GN.IE
Retrocopy ENQFTIESAEVVFPNGKSHTIPELT**KEVVISDPINK*VGTRAIPENFAKLLTRMDLKSEVIGYGN*IE

Parental  IEIPPTRADVIHACDIVEDAAIAYGYNNIQMALPKTYTIANQFPLNKLTELLRYDMAAAGFTE-ALTFAL
          IEI.PTRAD.IHACDIV.D.AIAYGY.NIQ.ALP.TYT..NQFPLNKL..LLR.D..AAGFTE..L.F.L
Retrocopy IEISPTRADIIHACDIVKDGAIAYGYSNIQVALPETYTVTNQFPLNKLRGLLRHDRVAAGFTE<RLGFRL

Parental  CSQEDIADKLGLDISATKAVHISNPKTAEFQVARTTLLPGLLKTIAANRKMPLPLKLFEISDIVVKDSSR
          C.Q...ADKLG.DISATKAVHIS......FQ.....LLPGLLKTIA.N..MPLPLK...ISD.VVK..SR
Retrocopy CPQGGVADKLGFDISATKAVHISDSTAI*FQMVHIALLPGLLKTIATNYMMPLPLK--QISDTVVKNASR

Parental  DVGARNYRHLCAVYYNKNPGFEIIHGLLDRIMQLLNVPPGEKKGGYVIKASEGAAFF
          DVG.RNYRHLCA.YY.KNP.FE.I.G.LDRI.QLL.VPPGEKKG..VI.ASEG..F.
Retrocopy DVGERNYRHLCAIYYSKNPWFETIRGFLDRIIQLLHVPPGEKKGDGVITASEGPSFW

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	54.29 RPM
SRP017611_kidney	0.00 RPM	31.84 RPM
SRP017611_liver	0.00 RPM	25.68 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1179 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1179 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011649	1 retrocopy	retro_btau_1451,
Felis catus	ENSFCAG00000026772	1 retrocopy	retro_fcat_1179 ,
Gorilla gorilla	ENSGGOG00000017051	1 retrocopy	retro_ggor_598,
Pteropus vampyrus	ENSPVAG00000006985	1 retrocopy	retro_pvam_804,