RetrogeneDB ID: retro_fcat_231

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:55628787..55629597(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSFCAG00000003665
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_fcat_231
TTACAAGGGAATTTGTATCTTTTTAGTGATATCAACATGATACACTTTGCTACCAATATGTACAAAAACCTTTATTCTGG
TGATATTCTGCATGCTTCGAGAGAAAAAAGAACCACAGTTGTTGCATGACTGAAATAGCTTCAGGCAGAAATGGAACCAA
TTGTGAAGACATTTGAAGATCCAGAAACTACAAGGCAGATGCAGTCAACCAGAGATGGGCAGATGCTGTTTAAGTACCTG
GTGGGCAGGCATGGTTTTAGGTAGGAATATTTAGATATACTCTAGAGTTATGTAAAATCCAATATGAATATGGGAATTAC
TCTGGAGCACCAGAATATCTTTACTTCTTTAGAATGTTGGTTCCAGCAACAGCCAGAAATGTTTTGAGTTCACTCAGGGG
AAAACCGGCCTCTGAAATCTTAATTCAGAGCAGGGATGCAGCAATGGAAGACCTTACATGGTTAAAAGAGACCATAGGTA
ATAATTCTGAGTTTTCCACTTCGGTATCTTCAGCAGCAAACAAGGTTCATCCACTGTCCTCTGTTTTCTTCAACTAATCA
AGGGGCATGATAACATTATTGATCTCTTCTTTTGCCAGCCATCATATCTTAATGCAATTTAGATGATATGCCCACATATT
CCTCGCTATTAGGCTACAGCCATCATAACGAACAAAGATGTTCAAAAATGCCAGCAGCTGCTAAAAGATCTGGTTAAAGT
TATTGAACACAGTCTTACACATATAAAGACCCAGTTACAGAATTTCTTGAATGCTTTTATGTTAACTTGGACTTTGATGG
AGCTCAGAAA

Alignment

ORF - retro_fcat_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHALREKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQST
          LQG.L.L.SD.NM..FA...YKNLYS.DI.HA.REKRTTVVA.LK.LQAE.EPIVK.FEDPETTRQMQST
Retrocopy LQGNLYLFSDINMIHFATNMYKNLYSGDILHASREKRTTVVA*LK*LQAEMEPIVKTFEDPETTRQMQST

Parental  RDGRMLFDYLADKHGFRQEYLDTLYRY-AKFQYECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASE
          RDG.MLF.YL...HGFR.EYLD.L..Y..K.QYE.GNYSGA.EYLYFFR.LVPAT.RN.LSSL.GK.ASE
Retrocopy RDGQMLFKYLVGRHGFR*EYLDIL*SY<CKIQYEYGNYSGAPEYLYFFRMLVPATARNVLSSLRGKPASE

Parental  ILMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQQRTWLIHWSLFVFFNHP-KGRDNIIDLFLYQPQYLNA
          IL.Q..DAAMEDLT.LKETI.NNS..S...S........H....VFFN...KG.DNIIDLF..QP.YLNA
Retrocopy ILIQSRDAAMEDLTWLKETIGNNSEFS--TSVSSAANKVHPLSSVFFN*S<KGHDNIIDLFFCQPSYLNA

Parental  IQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQ-ESYTYKDPITEFVECLYVNFDFDGAQK
          I...CPHI.RY..TA.ITNKDV.K..Q.LKDLVKVI....SYTYKDP.TEF.EC.YVN.DFDGAQK
Retrocopy I*MICPHIPRY*ATAIITNKDVQKCQQLLKDLVKVIEH<QSYTYKDPVTEFLECFYVNLDFDGAQK

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	66.34 RPM
SRP017611_kidney	0.00 RPM	269.81 RPM
SRP017611_liver	0.00 RPM	154.97 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_231 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_231 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 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231 ,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,