RetrogeneDB ID: retro_fcat_541

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:83639455..83640061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSFCAG00000011245
• Aliases: None
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_fcat_541
ATGACTATGGCCTATATCAGCTCAGATGGGGCCATATCCCTGCTGTCGTACACAGGAGATGACCAGTGGGAAGTGAAAAA
GATCAACAACACTCACATTATTGGCCGCAATGCAGTCAGTTGACCCCCTCCTTTTGAACCTGGAAGCCTCATAGTCCAGC
TATCGGTGCAGAAGCCCAACTGCATTAAGAAGTTTGCATCAAGTGGCTGTGACAACCTCATCAAGCTGTGGAAGGAAGAG
GAGACCAGCCAACAGAAGAAACAGAAGCTACAAGTGCACAGTGACTGGGTTTGAGATGTGGCCTGGGCCCTCTCCATTAG
CCTGCTCACCAGCACCATCACCAGCAGCTCCCAGGATGGTCATATGTTCATTTGGACCCATGACAATGCCTCAAGCAATA
TGTGGTTGCTCAAACTGCTGCATAAGTTCAATGATGTGTGGCATGTGAGCTGGTCCATCATGGCCAACATCCTGCCTTTC
TCAGGCAGAAATAATAAGGAGGCCCTGTGGAAGGAGTCCATCAATGGGCAGTGGGTGTGCACCAGTGATGTCAACAAGGC
CCAGGATTCTGTGCCTGCTTCCATCACAGCGGACGAGCAGAATGAG

Alignment

ORF - retro_fcat_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.1 %
• Parental protein coverage: 63.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKKFASGGC
          ...A..SSDGAISLL.YTG..QWEVKKINN.H.IG.NAVS..P...PGSLI.Q.S.QKPN.IKKFAS.GC
Retrocopy MTMAYISSDGAISLLSYTGDDQWEVKKINNTHIIGRNAVS*PPPFEPGSLIVQLSVQKPNCIKKFASSGC

Parental  DNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDISSNTWSPKL
          DNLIKLWKEEE..Q.K..QKL..HSDWV.DVAWA.SI.L.TSTI.S.SQDG..FIWT.D..SSN.W..KL
Retrocopy DNLIKLWKEEETSQQK-KQKLQVHSDWV*DVAWALSISLLTSTITSSSQDGHMFIWTHDNASSNMWLLKL

Parental  LHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSTSVTEGQQNE
          LHKFND.VWHVSWSI.ANIL..SG..NK..LWKES..GQWVC.SDVNK.Q.SV..S.T...QNE
Retrocopy LHKFND-VWHVSWSIMANILPFSGRNNKEALWKESINGQWVCTSDVNKAQDSVPASITADEQNE

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	16.99 RPM
SRP017611_kidney	0.00 RPM	91.62 RPM
SRP017611_liver	0.00 RPM	27.09 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_541 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_541 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541 ,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,