RetrogeneDB ID: retro_fcat_526

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:50555317..50556056(+)
• Located in intron of: ENSFCAG00000025121

Retrocopy information

• Ensembl ID: ENSFCAG00000027676
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSFCAG00000002105
• Aliases: None
• Description: general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653]

Sequence

>retro_fcat_526
ATGGCCAAACTTGAAGAACTCGATTTGACCGGTGCCAAACAGAACACCAGAGTATGGCTCATCAAGTTTCCCTAAATACT
TGTCCCAGCAATGGGCCGAAGCCTCTGAAAGAGGTAAAGTTGGGAAACTGCGGATTGCTAAGAATCAAGGAAGGACTGAG
GTGTCATTTACTTTGAATGAGGCTCTTGCAAATAGTCACGATATTGGCAGAAAACCAGCTTCTGTCAGCACTCCAGAGAA
CATCCATTTGTCTTACAAAGTGTTGGAGGACAGACCTTAACAGTCTTTACTGAGAGGCTCATCAAATAAACTTTCATTGG
AAGGAATAGTCGTACAAAGAGCTGAATGCCAACCTGCTGCCAGTGAAAACTACATGAGATTAAAGAGATTGCAAATAGAA
GAATCTTCCAAACCTGTAAGGCTATCACATCTGGACAAAGTTGTGACAACGAATTATAAACCTGTTGCTAATCATCAATA
CAATATTGAATATGAAAGGAAAAAGAAAGATGGAAAACGAGCTCAAGCTGATAAACATGTTTTAGACATGATATTTTCAG
CATTTGAGAAACATCAGTATTACAATCGTAAGGATTTGGTGGACATCACAAAACAACTTGTGGGGTACGTAAAGGAAATC
TTGAAAGAAATTGGTGTTCAGAATGTAAAAGGAATCCACAAAAACACATGGGAGCTGAAGCCAGAGTATAGACAGTATCA
AAGAGAAGAAAAGAGCGAT

Alignment

ORF - retro_fcat_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAERGELDLTGAKQNTGVWLVKVP-KYLSQQWAKAPGRGEVGKLRIAKNQGRTEVSFTLNEDLANIHDIG
          MA...ELDLTGAKQNT.VWL.K.P.KYLSQQWA.A..RG.VGKLRIAKNQGRTEVSFTLNE.LAN.HDIG
Retrocopy MAKLEELDLTGAKQNTRVWLIKFP>KYLSQQWAEASERGKVGKLRIAKNQGRTEVSFTLNEALANSHDIG

Parental  GKPASVSTP-REHPFVLQSVGGQTLTVFTE-SSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSK
          .KPASVSTP.REHPFVLQSVGGQTLTVFTE..SS.KLSLEGIVVQRAEC.PAASENYMRLKRLQIEESSK
Retrocopy RKPASVSTP<REHPFVLQSVGGQTLTVFTE>GSSNKLSLEGIVVQRAECQPAASENYMRLKRLQIEESSK

Parental  PVRLSQQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITK
          PVRLS..LDKVVTTNYKPVANHQYNIEYERKKK.DGKRA.ADK.HVLDM.FSAFEKHQYYN.KDLVDITK
Retrocopy PVRLS-HLDKVVTTNYKPVANHQYNIEYERKKK-DGKRAQADK-HVLDMIFSAFEKHQYYNRKDLVDITK

Parental  QPVGYLKEILKEIGVQNVKGTHKNTWELKPEYRHYQGEEKSD
          Q.VGY.KEILKEIGVQNVKG.HKNTWELKPEYR.YQ.EEKSD
Retrocopy QLVGYVKEILKEIGVQNVKGIHKNTWELKPEYRQYQREEKSD

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	9.99 RPM
SRP017611_kidney	0.00 RPM	8.45 RPM
SRP017611_liver	0.00 RPM	7.48 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_526 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_526 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
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753, retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526 ,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850,