RetrogeneDB ID: retro_fcat_623

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:68437385..68437906(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000029264
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSFCAG00000024719
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_fcat_623
GAAACCAAGAAAGAAACAAACGCCCCCAAGAAGAAGGAGAGTAAAATTAGTGTGAGCAAGAATTCTAAACTCCTCAGTAC
TAACGCAAAGAGGATTCAGAAGGAACTGGCAGACATCACTTTAGATCCTCCACCTAACTGTAGTGTTGGTCCCAAAGGTG
GTAACATCTATGAATGGAGATCCACCATGCTGGGGCCTCCAGGATCTGTATTTGAGGGCGGTATACTCCTCCTTTATACC
ACTTTTATACCAGAATACCCCTTTCAACCTCCAAAGGTTACATTTTGGACGATAACCTCTCACTGTAATATTAACAGTCA
AGGAGTTATTTGCTTCGACATATTAAGAAGATAATTGGAGTACAGCACTAACCTTTTCTAAAGTTCCCCTTTCTATCTTC
TCCCTTCTTAACAGACTGCAATCCTGCTGACCCTTTGGTGCATAGTGTTGCCATTGACTATATGACCAACAGAGCAGAAC
ATGATAGAATGGCCAGACAGTGGACCAAGAGATATGCTACA

Alignment

ORF - retro_fcat_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.14 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTEKETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSV
          .T.KETN.PKKKESK.S.SKNSKLLST.AKRIQKELADITLDPPPNCS.GPKG.NIYEWRST.LGPPGSV
Retrocopy ETKKETNAPKKKESKISVSKNSKLLSTNAKRIQKELADITLDPPPNCSVGPKGGNIYEWRSTMLGPPGSV

Parental  YEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILK-DNWSPALTISKVLLSICSL-LTD
          .EGG...L..TF.PEYPF.PPKVTF.T...HCNINSQGVIC.DIL..DNWS.ALT.SKV.LSI.SL.LTD
Retrocopy FEGGILLLYTTFIPEYPFQPPKVTFWTITSHCNINSQGVICFDILR>DNWSTALTFSKVPLSIFSL>LTD

Parental  CNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          CNPADPLV.S.A..YMTNRAEHDRMARQWTKRYAT
Retrocopy CNPADPLVHSVAIDYMTNRAEHDRMARQWTKRYAT

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	64.85 RPM
SRP017611_kidney	0.00 RPM	38.34 RPM
SRP017611_liver	0.00 RPM	23.86 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_623 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_623 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623 ,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106, retro_fcat_785,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,