RetrogeneDB ID: retro_fcat_1636

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:60409188..60409889(-)
• Located in intron of: ENSFCAG00000005289

Retrocopy information

• Ensembl ID: ENSFCAG00000031723
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSFCAG00000011368
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_fcat_1636
GAAATGGTGGAATCGATGAAGAAAGTACAGGGATGGATGTGGAGTTGACAGTTGAAGAAAGAAACCTCCTATCTGTTGCA
TATAAAAATGTGATTGGAGCCAGAAGAGCTTCCTGGAGAATAATCAGCAGCATTGAACAGAAAGAAGAAAACAAGGGAGG
AGAAGACAAACTAAAAATGATTCGGGAATATCGGCAAATGGTTGAGACTGAGCTAAAGTTAATCTGTTGTGACATTCTGG
ATGTACTGGACAAACACCTCATTCCAGCAGCCAACACTGGCGAGTCCAAGGTTTTCTATTATAAAATGAAAGGGGACTAC
CACAGGTATCTGGCTGAATTTGCCACAGAAAATGACAGGAAGGAGGCTGCGGAGAACAGCCTAGTGGCTTATAAAGCTGC
TAGTGATATTGCAATGACAGAACTTCCACCAACGCATCCTATTCGCTTAGGTCTTGCTCTCAATTTCTCCGTATTCTCCT
ATGAAATTCTTAATTCCCCTGACCGTGCCTGCAGGTTGGCAAAAGCAGCTTTTGATGATGCAATTGCAGAACTGGATACG
CTGAGCGAAGAAAGCTATAAGGACTCTACACTTATCATGCAGTTGTTACGTGATAATCTGACACTATGGACTTCAGACAT
GCAGGGTGATGGTGAAGAGCAGAATAAAGAAGCGCTGCAGGATGTGGAAGATGAAAATCAG

Alignment

ORF - retro_fcat_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMVESMKKV-AGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVE
          EMVESMKKV..GMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVE
Retrocopy EMVESMKKV<TGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVE

Parental  TELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAM
          TELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFAT.NDRKEAAENSLVAYKAASDIAM
Retrocopy TELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATENDRKEAAENSLVAYKAASDIAM

Parental  TELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTL
          TELPPTHPIRLGLALNFSVF.YEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTL
Retrocopy TELPPTHPIRLGLALNFSVFSYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTL

Parental  WTSDMQGDGEEQNKEALQDVEDENQ
          WTSDMQGDGEEQNKEALQDVEDENQ
Retrocopy WTSDMQGDGEEQNKEALQDVEDENQ

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	4.82 RPM	265.47 RPM
SRP017611_kidney	2.68 RPM	135.01 RPM
SRP017611_liver	1.52 RPM	67.83 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1636 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1636 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636 ,
Felis catus	ENSFCAG00000032017	4 retrocopies	retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,