RetrogeneDB ID: retro_fcat_1680

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:2190496..2191117(+)
• Located in intron of: ENSFCAG00000022240

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A36
• Ensembl ID: ENSFCAG00000027489
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 [Source:HGNC Symbol;Acc:25554]

Sequence

>retro_fcat_1680
GGGGCTGGTCGCACATGTCCACTGAAAGTTATAGTAACACAGCTATGGTCTTCTGCTGTGATGCTTTCTACCTCTGAAGT
TCAGCTGAACACACGGCTTAGACCTAGTGTCTACTAAACCCGTCTCTTCTGGACCTTTACAGTGCCTAAATGTGACCCTG
GAAAAAGGAAGGTCTGTTCCTTGTTTAGAGGATCAGGCCCCAATTGAATGGAGGTGGCTTCTTCCCGAGCAACATTCTTT
GCTGCTGATTCAAACTGTGAGAAAAAGTCGAATGATGTAGTAGATCCTCATTTTACCTGTCACATGACTTCAGCTGCAGT
GGCCTGTTTTACTATACCCACAGCAACCAATCCCATTTGGCTAAGAAAGAACTGGTTACAGCTTGATACAAGGAACTATG
AAAAACAAATGGGTACTTTTTAATGTGCTCATAAAGTGTAGCAGACACATGCCCAAAGAAGACTTTATAGGAGGAGATCA
GCCTCGGGTTCACAGAACTTTATTCATTTGGTTATTTGTAGAAGTATTAAGCAAAAACTACTAGAATAAAAGATGACTTT
GATAATGGAAGATGATGAAGAGTCTGTGAAAGAAATACCAAATTTTGTGGGACTGATGCTG

Alignment

ORF - retro_fcat_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 68.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAILTCPLEVVKTRLQSSSVTLYISEVQLNTMAGASV-NRVVSPGPLHCLKVILE-KEGPRSLFRGLGPN
          GA..TCPL.V..T.L.SS.V.L..SEVQLNT....SV....VS.GPL.CL.V.LE.K....SLFRG.GPN
Retrocopy GAGRTCPLKVIVTQLWSSAVMLSTSEVQLNTRLRPSV>TKPVSSGPLQCLNVTLE<KRKVCSLFRGSGPN

Parental  LVGVAPSRAIYFAAYSNCKEKLNDIFDPDSTQVHMISAAMAGFTAITATNPIWLVKTRLQLDARNRGEKR
          ...VA.SRA..FAA.SNC..K.ND..DP..T..HM.SAA.A.FT..TATNPIWL.K..LQLD.RN..EK.
Retrocopy *MEVASSRATFFAADSNCEKKSNDVVDPHFT-CHMTSAAVACFTIPTATNPIWLRKNWLQLDTRNY-EKQ

Parental  MGAFECIRKVYQTDGLKGFYRGMSASYAGISETVIHFVIYESIKQKLLEYKIASTMENDEESVKEASDFV
          MG.F.C..KV.QT......YR..SAS....S...IH.VI..SIKQKLLE.K....ME.DEESVKE...FV
Retrocopy MGTF*CAHKV*QTHAQRRLYRRRSASG---SQNFIHLVICRSIKQKLLE*KMTLIMEDDEESVKEIPNFV

Parental  GMML
          G.ML
Retrocopy GLML

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	0.23 RPM	74.14 RPM
SRP017611_kidney	0.52 RPM	49.26 RPM
SRP017611_liver	0.10 RPM	6.57 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1680 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1680 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680 ,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,