RetrogeneDB ID: retro_fcat_840

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B3:60700457..60701283(+)
• Located in intron of: ENSFCAG00000002880

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSFCAG00000001572
• Aliases: None
• Description: cyclin B1 [Source:HGNC Symbol;Acc:1579]

Sequence

>retro_fcat_840
CTTGGTAACAAAGTCAGTGAACAGCCACAAGCCAAATTGCCTCTGAAAAAGGAAGCAAAAACTTTGGCTCCTGGAAAAGT
TATTGCTAAAAAAATATCAAAACTTCAAAGCACCTGAGCCTGTGTCTGTACCTGTGCCCCAACTAGAGCCAGAACATGAG
CCTGTTAAAGAAGAAAAACTTTCTCCGGAGCCTATTTTGGTCGATACTCCATCTCCAAGCCCAGTGGAAATGTCTGGATG
TGCTCCTGCAGAAGAATATCTGTGTCAGTCTCTCTCTGATGTAATTCTTACAGTGAATGATGTGGATGCAGAAAATGGAG
CTGATCCAAACCTTTGTAGTGAATATGTGAAAGATATTTATGCTTATCTGAGACAACTTGAGGAAGAGCAAGCAGTAAGA
CCAAAATACCTACTGGGTCGTGAAGTCACTGGAAATATGAGAGCCATCCTAATTGACTGGCTAGTGCAGGTTCAAATGAA
ATTCAGGTTACTGCAGGAGACCATGTACATGACTGTTTCCCTTATTGATCGGCTCATGCAGAATAATTGTGTACCCAAGA
AGATGATGTAGCTGGTTGGTGTCACTGCCATGTTTATTGCAAGTAAATACGAAGAAATGTACCCTCCAGAAATTGGTAAC
TTTGCCTTTGTGACTGACGACTCTTACACCAAGCACCAAATCAGACAGATGGAAATGAAGATTCTAAGATCTTTACATTT
TGGTCTGGGCCGCCCTCTACCCCTGCATTTCCTTTGGAGAGCATCTAAGATTGGAGAGGTTGGTGTTGAGCAACATACTT
TGGCCAAATACCTGATGGAACTAACT

Alignment

ORF - retro_fcat_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.57 %
• Parental protein coverage: 64.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGNKVSEQPQAKLPLKKEAKTLAPG-KVIAKKIPKPLDKAPEPVSVPVPEPEPEHEPVKEEKLSPEPILV
          .GNKVSEQPQAKLPLKKEAKTLAPG.K...KK......KAPEPVSVPVP..EPEHEPVKEEKLSPEPILV
Retrocopy LGNKVSEQPQAKLPLKKEAKTLAPG>KLLLKKYQN--FKAPEPVSVPVPQLEPEHEPVKEEKLSPEPILV

Parental  DTPSPSPMETSGCAPAEEYLCQAFSDVILAVNDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVRPKYL
          DTPSPSP.E.SGCAPAEEYLCQ..SDVIL.VNDVDAE.GADPNLCSEYVKDIYAYLRQLEEEQAVRPKYL
Retrocopy DTPSPSPVEMSGCAPAEEYLCQSLSDVILTVNDVDAENGADPNLCSEYVKDIYAYLRQLEEEQAVRPKYL

Parental  LGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMY
          LGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVS.IDR.MQNNCVPKKM..LVGVTAMFIASKYEEMY
Retrocopy LGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSLIDRLMQNNCVPKKMM*LVGVTAMFIASKYEEMY

Parental  PPEIGDFAFVTDNTYTKHQIRQMEMKILRSLNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELT
          PPEIG.FAFVTD..YTKHQIRQMEMKILRSL.FGLGRPLPLHFL.RASKIGEV.VEQHTLAKYLMELT
Retrocopy PPEIGNFAFVTDDSYTKHQIRQMEMKILRSLHFGLGRPLPLHFLWRASKIGEVGVEQHTLAKYLMELT

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	1.49 RPM
SRP017611_kidney	0.00 RPM	1.86 RPM
SRP017611_liver	0.00 RPM	6.17 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_840 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_840 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Felis catus	ENSFCAG00000000138	1 retrocopy	retro_fcat_809,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840 ,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,