RetrogeneDB ID: retro_cfam_278

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:98103228..98104090(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSCAFG00000005118
• Aliases: None
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_cfam_278
AGGTCCGTCAAAATCTTCAATGTGCGAAATGGAGGACAGATCCTTATTGCCAACCTCAGAGGTCACGAGGGTCCTGTGTG
GCAAGTGGCCTGGGCCCACCCCATGTATGGCAACATCCTGGCATCCGGCTCCTATGACCGGAAAGTCATTATCTGGAAGG
AGGAGAATGGCACCTGGGAGAAGACTCTGAGCACACAGGACACGACTCCTCAGTAAACTCTGTGTGCTGGGCCCCCCATG
ACTACAGCCTAATACTGGCCTGTCGGAGCTCAGATGGGGCCATCTCCCTGCTGACATACACCGGAGAGGGCCAGTGGGAA
GTAAAGAAGATCAACAATGCTCATACTATTGACTGCAATGCCATCAGTTGGGCCCCTGCTGTTGTACCTGGAAGCCTCAT
AGACCAGCCATCGGAACAGAAGCCCAACTACATCAAGGGGTTTGCTTCAGGCGACTGTGACAACCTCATCAAACTGTGGA
AGGAAGAGGCGGATGGCCAGTGGAAGGAGGAACAGAAGCTAGAAGCGCACAGTGACTGGGTTCGAGATGTGGCCTGGGCC
CCCTCCATTGGCCTGCCCACCAGCATCATCGCCAGTTGCTCCCAGGACGGTCGTGTGTTCATCTGGACTTGTGATGACAC
CTCAGGCAATACATGGTCACCCAAACTTTGCACAAGTTCAATGATGTTGGGTGGCATGTGAGCTGGTACATCACAGCCAA
CATCCTGGCTGTCTCGGGCGGAGACAATAAGGTGACCCTGTGGAAGGAGTCCGTTGACAGACAGTGGGTGTGCATCAGTG
ATGTCAACAAGGGCCAGGGATCTCTGTCTGCTTCTGTCACAGAGGGCCAGCAGAACGAGCAA

Alignment

ORF - retro_cfam_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.45 %
• Parental protein coverage: 89.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMYGNILASCSYDRKVIIWKEENGTWEKT-HEHTGHD
          RSVKIF.VRNGGQILIA.LRGHEGPVWQVAWAHPMYGNILAS.SYDRKVIIWKEENGTWEKT..EHTGHD
Retrocopy RSVKIFNVRNGGQILIANLRGHEGPVWQVAWAHPMYGNILASGSYDRKVIIWKEENGTWEKT<SEHTGHD

Parental  SSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDQPSG
          SSVNSVCWAPHDY.LILAC.SSDGAISLLTYTGEGQWEVKKINNAHTI.CNA.SWAPAVVPGSLIDQPS.
Retrocopy SSVNSVCWAPHDYSLILACRSSDGAISLLTYTGEGQWEVKKINNAHTIDCNAISWAPAVVPGSLIDQPSE

Parental  QKPNYIKKFASGGCDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIW
          QKPNYIK.FASG.CDNLIKLWKEE.DGQWKEEQKLEAHSDWVRDVAWAPSIGLPTS.IASCSQDGRVFIW
Retrocopy QKPNYIKGFASGDCDNLIKLWKEEADGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSIIASCSQDGRVFIW

Parental  TCDDTSGNTWSPKL-LHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSA
          TCDDTSGNTWSPKL.LHKFNDV.WHVSW.ITANILAVSGGDNKVTLWKESVD.QWVCISDVNKGQGS.SA
Retrocopy TCDDTSGNTWSPKL<LHKFNDVGWHVSWYITANILAVSGGDNKVTLWKESVDRQWVCISDVNKGQGSLSA

Parental  SVTEGQQNEQ
          SVTEGQQNEQ
Retrocopy SVTEGQQNEQ

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
SRP012049_cerebellum	0.08 RPM	30.11 RPM
SRP017611_brain	0.00 RPM	20.72 RPM
SRP017611_kidney	0.00 RPM	56.86 RPM
SRP017611_liver	0.00 RPM	16.17 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_278 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_278 has 0 orthologous retrocopies within eutheria group .

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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,