RetrogeneDB ID: retro_fcat_522

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:30592107..30593081(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023720
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPS6
• Ensembl ID: ENSFCAG00000003561
• Aliases: None
• Description: COP9 signalosome subunit 6 [Source:HGNC Symbol;Acc:21749]

Sequence

>retro_fcat_522
GGCGCGGGGAAAATGGCGGCGGCGGCGAACAGGACCGGAGGGAACAGCCGGGATGGAGGTGGATGCAGCAGTAGTCCCCA
ACGTGATGGCCTCCGGCGTGACAGGGAGCGTCTCAGTCCTCTTCATCCCCTTGTCATTCTCAACATTTCAGACCATTGGA
TTCGTATGCGCTCCCGGGAGGGGTGGCCTATGCAGGTGATTGGGACTCTGATCGGGAAACAGGAGGGCCGAAATATCGAG
GTGATGAACTCCTTTGAGCTGCTGTCCCACGCCGTGGAAGAGAAGATTATCATTGACAAGGAGTGTTACTACACCAAGGA
GGAGCAGTTCAAACAGGTGTTCAAGGAGCTGGAGCTTCTGGGTTGGTATACCCCCGGGGGGCCGCCTGACCCCTCTGACA
TCCACCTCCAGAAGCAGGCATGCGAGATCATCCAGAGCCCTCTCTTTCTTAAGTTGAACCCTATGACCAGGCACACACAT
CTTCCCAACAGTGTTTTTGAGTCTGTCATCGATATAATCAATGCAGAGGCCACAATGTTGTTTGCTGAGCTGACCTACAC
TCTGGCCACAGAGGAAGCTGAACGCATCGGTGTAAACCACGTAGCCGGAATGATAGCCACAGGCCGTGGGGAGAACTCCA
CTGTGGCTGAACACCTGATAGAGCAACACAGTGCTATTAAGATGCTGCACAGCCGGGTCAAGCTCATCTGGGAATACGTT
AAGGCCTCTGAAGCAGGGGAGGTCCCCTTTAATCAAGAAATCCTGCGGAGGCCTATGCTCTGTGTCACTGCCTCCCAGTG
TTCAGCACAGACAAGTTCAAGACAGACTTTTACGATCAATGTAATGACGTGGGGCTCGTGGCCTACCTTGGCACCATCAG
CAAAACGTGCAACACCATGAACCAGTTTGTGAACAAGTTCAACGTCCTCTATGATCGACAAGGCATCGGCAGGTGGATGC
AGGGGCTCTTCTTC

Alignment

ORF - retro_fcat_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAGKMAAAANGTGGSS-GMEVDAAVVPSVMASGVTGSVSVA-LHPLVILNISDHWIRMRSQEGRPMQVIG
          GAGKMAAAAN.TGG.S.GMEVDAAVVP.VMASGVTGSVSV..LHPLVILNISDHWIRMRS.EG.PMQVIG
Retrocopy GAGKMAAAANRTGGNS>GMEVDAAVVPNVMASGVTGSVSVL<LHPLVILNISDHWIRMRSREGWPMQVIG

Parental  ALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLGWYTTGGPPDPSDIHVHK
          .LIGKQEGRNIEVMNSFELLSH.VEEKIIIDKE.YYTKEEQFKQVFKELE.LGWYT.GGPPDPSDIH..K
Retrocopy TLIGKQEGRNIEVMNSFELLSHAVEEKIIIDKECYYTKEEQFKQVFKELELLGWYTPGGPPDPSDIHLQK

Parental  QVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEATMLFAELTYTLATEEAERIGVDHVARMTATG
          Q.CEII.SPLFLKLNPMT.HT.LP.SVFESVIDIIN.EATMLFAELTYTLATEEAERIGV.HVA.M.ATG
Retrocopy QACEIIQSPLFLKLNPMTRHTHLPNSVFESVIDIINAEATMLFAELTYTLATEEAERIGVNHVAGMIATG

Parental  SGENSTVAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVPFNHEILR-EAYALCHCLPVLSTDKFKTDF
          .GENSTVAEHLI.QHSAIKMLHSRVKLI.EYVKASEAGEVPFN.EILR.EAYALCHCLPV.STDKFKTDF
Retrocopy RGENSTVAEHLIEQHSAIKMLHSRVKLIWEYVKASEAGEVPFNQEILR<EAYALCHCLPVFSTDKFKTDF

Parental  YDQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIGRRMRGLFF
          YDQCNDVGL.AYLGTI.KTCNTMNQFVNKFNVLYDRQGIGR.M.GLFF
Retrocopy YDQCNDVGLVAYLGTISKTCNTMNQFVNKFNVLYDRQGIGRWMQGLFF

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	74.26 RPM
SRP017611_kidney	0.00 RPM	135.11 RPM
SRP017611_liver	0.00 RPM	32.05 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_522 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_522 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389,
Felis catus	ENSFCAG00000003561	1 retrocopy	retro_fcat_522 ,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Monodelphis domestica	ENSMODG00000004170	1 retrocopy	retro_mdom_220,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690,