RetrogeneDB ID: retro_fcat_1889

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: JH409055.1:67350..67922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSFCAG00000000591
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_fcat_1889
GAATTTAGGAGGAAGGCTGACTATCAGTACCAACTCTTGCAATATAATGTAGACTTCTTAAATATAAGTTGGCTAGAACT
GACATTTATGAATGAGCAAAGAGAATACCCTCCAACAACTTCAACTTGGTAGTTTAATTTTAAATTTAATTTGATGGAGT
ACATGTATTCCCAGGACTCTATAGTGATACTAAAAACATCTGGTATCCATTTTTAAAAACGTGAGGAAGGAATTGAGACC
CATTACTTCACAGAACTTCTTATGACATCAGGAGTGGTCCTCTGCAAAGGGGTCAAATGGTTATAATTTCACAGTGGTTA
TGATTTTGGCTATTTAATCAAAATCCTGACCAACTCTAACTTGCCTGAAGAAGAACTAGACTTCTTTGAGATCCTTCAAT
TATTTATTTCTAATAATTTATGATGTGAAGTACTCCCTGAAAAATGGCAAAAAATCTCAAAGGTGGTTTATGGGAAGCTG
CTCAACAGTTACAGCTGGAACTGATAGGACCACAACATCAGGCAGGATCTGATTAATTGTTCACAGGAATGACCTTTTTG
AAAATGAGAGAA

Alignment

ORF - retro_fcat_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.2 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQ
          EFR..ADYQYQLL..NVD.L.I..L.LTFMNEQ.EYPP.TSTW.FNFKFNL.E.MY.QDSI..L.TSGI.
Retrocopy EFRRKADYQYQLLQYNVDFLNISWLELTFMNEQREYPPTTSTW*FNFKFNLMEYMYSQDSIVILKTSGIH

Parental  FKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLF-FPV
          F.K.EE.GIET.YF.ELLMTSGVVLC.GVKWL.FHSGYDFGYLIKILTNSNLPEEELDFFEIL.LF.F..
Retrocopy F*KREE-GIETHYFTELLMTSGVVLCKGVKWL*FHSGYDFGYLIKILTNSNLPEEELDFFEILQLF>FLI

Parental  IYDVKYLMKS-CKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMRE
          IYDVKY..K...KNLKGGL.E.A.QL.LE.IGPQHQAGSD.L.TGM.F.KMRE
Retrocopy IYDVKYSLKN>AKNLKGGLWEAAQQLQLELIGPQHQAGSD*LFTGMTFLKMRE

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	43.50 RPM
SRP017611_kidney	0.00 RPM	24.84 RPM
SRP017611_liver	0.00 RPM	17.08 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1889 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1889 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
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889 ,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,