RetrogeneDB ID: retro_fcat_333

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:85608839..85609661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSFCAG00000002780
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_fcat_333
ATGACACCCTCCAGGAGTCTCATGGTCCTGTAGCAGGGCTCCTGCTGTTGTTTTGTGGGGTTTCCTGGACCCATGTGCAG
TAGAGTGACGTGCCCAACATCATGGCAAGAACAGGAGAGAGTTGCTGGAAGGAGAATGGATGATAGAATTTTATGTTCCA
TGGTGTCTTTCTTGTCAGAATCTACAACCAGAATGGAGAAGTTTTGCTTAACGGGGAGAACATCTTGAGGTTAATGTTGC
AAAAGGGGATGTCATAGAGCAGCCAGGACTGAGTGGATGGTTTATCATAACTGCCCTTCCTTCCATCTACTATTGTTAAG
ATGGTGAATTTAGGTGCTATCAGGGCTCAAGGAATAAGAAGGACTTCATAAACTATAAATGAGAAAGAGTGGAAAAGTAC
TGAACCCATTTCATCATGGTTTGGCCCAGATTCTGTTCTGATGAATAGTATGGCAGCACTCTTTCAGCTATCTTCATGGA
TCAGGACTTGCTGTAACTATTTTATTGAAGACCTTTGATTATGGGTTTGGGGATAATGCACAATTTTTGCTTTTAGCAAC
TCTGCTTTCAGGACTATCATTGGGACTCTGTATAATATTTGTGCTGCACTGCCTTTTTCCTTCAAAAAGATACAGATGAA
GCCATACCCTTCCCCCCCAAAATAATTATTATCAGAATCTTCTCAACCTTTGAAAAAAGTGCAGTAACAAGAAGCTCATG
AAAATGCTTCAGAAGAGGAAGCAGAAGGAAGGAACCAACAGACTTTCCACAGAATGCCACAGACAATGTCCTGTGGGTCC
TTCCTTGTTCACAGATAAATCC

Alignment

ORF - retro_fcat_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MTASRSPVV-PVAVLLLLACGAPWTHGRRSDVRIIT-DENWKELLEGEWMIEFYAPWCPACQNLQPEWES
          MT.SRS..V.PVA.LLLL.CG..WTH...SDV..I....N..ELLEGEWMIEFY.PWC..CQNLQPEW.S
Retrocopy MTPSRSLMV<PVAGLLLLFCGVSWTHVQ*SDVPNIM<GKNRRELLEGEWMIEFYVPWCLSCQNLQPEWRS

Parental  FAEWGEDLEVNVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFVSE-KEWKSIEP
          FA..GE.LEVNVAK.DV.EQPGLSG.FIITALP.IY.C.DGEFR.YQG.R.KKDFIN...E.K..K...P
Retrocopy FA*RGEHLEVNVAKGDVIEQPGLSGWFIITALPSIYYC*DGEFRCYQGSRNKKDFINYK*E<KSGKVLNP

Parental  -VSSWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFA-LATLLSGLLLGLCMIFVADC
          ..SSWFGP.SVLM.SM.ALFQLS.WIRTC.NYFIEDL.L.VWG..T.FA.LATLLSGL.LGLC.IFV..C
Retrocopy <ISSWFGPDSVLMNSMAALFQLSSWIRTCCNYFIEDL*LWVWG*CTIFA>LATLLSGLSLGLCIIFVLHC

Parental  LFPSKRRR-PQPYPSSKEKLLPESSQPLKKVEEEQEADEEDVSEEEAGS-KEGTNKDFPRNAI-RQRSVG
          LFPSKR.R...PYPS....LL.ESSQPLKKV...QEA..E..SEEEA...KE.T...FP.NA..RQ..VG
Retrocopy LFPSKRYR<MKPYPSPPK*LLSESSQPLKKV-Q*QEA-HENASEEEAEG<KEPTD--FPQNAT<RQCPVG

Parental  PSLATDQS
          PSL.TD.S
Retrocopy PSLFTDKS

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	8.26 RPM
SRP017611_kidney	0.00 RPM	11.95 RPM
SRP017611_liver	0.00 RPM	10.92 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_333 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_333 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333 ,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,