RetrogeneDB ID: retro_fcat_574

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:141559128..141559870(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSFCAG00000008944
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_fcat_574
ATGCATTGCCACAGAGTGGGAGCTGGTCCCATCGCCAAGAAGAAACTTGCAGAGGCCAAATATAAGAAGTGAGGAACTGC
CTTGGCTGAGGACCAGCTGGCCCAGATGTCAAAGCAGTTGGACATGTTCAAGACTAACCTGGAGGAATTTGCCAGCAGCA
CAAGCAGGAAATTCAGAAGAATCCCGAATTCTGGGTGCAGTTCCAGGACACGTGTGCCACCGTTGGGGTGATCCTCTGCC
CTCTGGAAGAGGATTTTGGCCCAAGATGGTAGGTGTGGGAGATTTCTATTATGAGCTGGGAGTCCAGATTATTGAAGTGT
GCCTGACCCTGAAGCACAGGGATGGAGGTGTGATAACTCTGGAGAAACTACAACAACAGGTGTTCAAAAGGAAGGGGCAG
CTTCACACAGGATATCAGCCAAGACAACCTGATCAGGGCCGTCAAGACACTAAAGGCACCTGCCACTGGCTTCCGGCATC
ATCTCTGCGGGTGGCACCTACCTCATTCAGTCTGTTCCAGCTGAGCTCAATATGGATCACACTGTGGTGCTGCAGCTGGC
AGAGAAAAATGGCTACGTGACTGTCAGTGATATCAAAGCCAGTCTTAAGTGGGAGGCCAAATGAGCCCGGCAAGTGCTAG
AACACCTGCTGAAGGAACAGCGGGCCTGGCTGGGACCTGCAGGCCCCTGAGGAGACTCACCACTGGCTGCCAGCTCTCTT
CACTGACCTCTGCTCCTAGGAG

Alignment

ORF - retro_fcat_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGXLQTSRLLQAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFAS-KHKQEIRKNPEFRVQFQ
          MH...VGAG......L..AKYK..GT.LAEDQLAQMSKQLDMFKTNLEEFAS..HKQEI.KNPEF.VQFQ
Retrocopy MHCHRVGAGPIAKKKLAEAKYKK*GTALAEDQLAQMSKQLDMFKTNLEEFAS<QHKQEIQKNPEFWVQFQ

Parental  DMCATIGV-DPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLK-GRGKFAQ
          D.CAT.GV.DPL.SG.GFW..M.GVGDFYYELGVQIIEVCL.LKHR.GG.ITLE.L.QQV.K.GRG.F.Q
Retrocopy DTCATVGV<DPLPSGRGFWPKMVGVGDFYYELGVQIIEVCLTLKHRDGGVITLEKLQQQVFK>GRGSFTQ

Parental  DVSQDDLIRAIKKLKALGTGF-GIIPVGGTYLIQSVPAELNMDHTVVLQLAEKSGYVTVSDIKASLKWET
          D.SQD.LIRA.K.LKA..TGF.GII..GGTYLIQSVPAELNMDHTVVLQLAEK.GYVTVSDIKASLKWE.
Retrocopy DISQDNLIRAVKTLKAPATGF>GIISAGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSDIKASLKWEA

Parental  ERARQVLEHLLKEGLAWL-DLQAPGEAHYWLPALFTDLYSQE
          ..ARQVLEHLLKE..AWL.DLQAP.E.H.WLPALFTDL.S.E
Retrocopy K*ARQVLEHLLKEQRAWL>DLQAPEETHHWLPALFTDLCS*E

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	21.35 RPM
SRP017611_kidney	0.00 RPM	34.11 RPM
SRP017611_liver	0.00 RPM	16.48 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_574 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_574 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574 ,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,