RetrogeneDB ID: retro_cfam_2011

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:53816009..53817305(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000028727
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TADA3
• Ensembl ID: ENSCAFG00000005324
• Aliases: TADA3, TADA3L
• Description: transcriptional adaptor 3 [Source:HGNC Symbol;Acc:19422]

Sequence

>retro_cfam_2011
ATGAGTGTACTGAAGGACTGCCCCTTGCAGTTCCATGACTTCAAGTCTGTGGACCACCTGAAGGTCTGTCCATGCTACAC
GGCTATGCTAGCCCGCTCTGAGGATGATGGCATCGGCATTGAAGAGCTGGAAACTCTGCAGCTGGAGCTTGAGACCCTGC
TTTCCTCTGCCAGCTGGTGCCTGTGGGTTCTTGAGGCCGAAACCCAGATCCTCACTGACTGGCAGGATAAGAAAGGTGAT
TGATGATTCCTGAAGCTGGGTCGAAACCATGAGCTTGGAGCTTCCCCCAAAACATGGAAAGCCGAAGAAGCAGAAACTGG
AAGGAAAGGTGGGACATGGGCTGGGCCCTGGTCCCCGGCATCCCAAATCCAGAAACCTTCAGCCCAAGATCCAGGAATAT
GAATTCACTGATGACCCAATTGACATGCCACGGATCCCCAGGAATGATGCCCCCAACAGGGTTTGGGCCTCTGTAGAGCC
CTACTGTGCTGATATCACCAGTGAGGAAGTACGCATACTAGAGGAACTACTAAACCCCCAGAAGACGAGGCTGAACATTA
CAAGATCCCACCCCTGGGGAAGCACTGCTCCCAATGCTGGGTACAGGAGGACCTGCTGGAGGAACAGAAGGATGGGGCCC
GGGCAGCAGCTGTGGCTGACAAAAAGAAAGGCCTTATGGGGCCACTGACTGAACTGGACACTAAAGATGTGGATGCCCTG
CTGAAGAAGTCTGAGGCCCAGCATGAGTAGCCTGAAGATGGGTGCCCTTTTGGTGCTCTGACGCAGCACCTCCTACAGGC
CCTGGTGGAGGAAAATATCATTTCCCCTATGGAGGATTCTCCTATTCCTGACATGTCTGGGAAGGAATCAGGGGCCAATG
GGGCAAGCACCGCTCCCTGTAATCAGAACAAGCCCTTCAGCGTGCCACATACCAAGTCCCTGGAGAGGCACATCAAGGAG
GAGCTGATTGCCCGGGGCCTGCTAGAGTCTGAGGACCGCCCTGCAGAGGACTCGAAGGATGAAGTCCTTGCCAAGCTGCA
CAAACTGCAGACCGAGCTGAAGGTGCTCAGTGCCCATAATCGTACCAAGAAGCACAACCTGATGAGGCTGGCAAAAGAGG
AGGTAAGCCAGCAGGAGCTGAGGCAGCGGGTCCACATGGCAGACAACGAGGTCATGGACGCCTTCTGGAAGATCATGGCT
GCCCGGCAGAAGAAGCAGACCCCAACCAAGAAGGAGAAGGACCAGGCCTGGAAGACTCTGAAGGAGCCTGAGAGCATCCT
AAAGCTGCTGGATGGG

Alignment

ORF - retro_cfam_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSELKDCPLQFHDFKSVDHLKVCPRYTAVLARSEDDGIGIEELDTLQLELETLLSSASRRLRVLEAETQI
          MS.LKDCPLQFHDFKSVDHLKVCP.YTA.LARSEDDGIGIEEL.TLQLELETLLSSAS..L.VLEAETQI
Retrocopy MSVLKDCPLQFHDFKSVDHLKVCPCYTAMLARSEDDGIGIEELETLQLELETLLSSASWCLWVLEAETQI

Parental  LTDWQDKKGDRRFLKLGRDHELGA-PPKHGKPKKQKLEGKAGHGPGPGPGRPKSKNLQPKIQEYEFTDDP
          LTDWQDKKGD..FLKLGR.HELGA.PPKHGKPKKQKLEGK.GHG.GPGP..PKS.NLQPKIQEYEFTDDP
Retrocopy LTDWQDKKGD**FLKLGRNHELGA>PPKHGKPKKQKLEGKVGHGLGPGPRHPKSRNLQPKIQEYEFTDDP

Parental  IDVPRIPKNDAPNRFWASVEPYCADITSEEVRTLEELL-KPPEDEAEHYKIPPLGKHYSQRWAQEDLLEE
          ID.PRIP.NDAPNR.WASVEPYCADITSEEVR.LEELL.KPPEDEAEHYKIPPLGKH.SQ.W.QEDLLEE
Retrocopy IDMPRIPRNDAPNRVWASVEPYCADITSEEVRILEELL<KPPEDEAEHYKIPPLGKHCSQCWVQEDLLEE

Parental  QKDGARAAAVADKKKGLMGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQALVEENIISPME
          QKDGARAAAVADKKKGLMGPLTELDTKDVDALLKKSEAQHE.PEDGCPFGALTQ.LLQALVEENIISPME
Retrocopy QKDGARAAAVADKKKGLMGPLTELDTKDVDALLKKSEAQHE*PEDGCPFGALTQHLLQALVEENIISPME

Parental  DSPIPDMSGKESGADGASTSPRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELRK
          DSPIPDMSGKESGA.GAST.P.NQNKPFSVPHTKSLE..IKEELIA.GLLESEDRPAEDS.DEVLA.L.K
Retrocopy DSPIPDMSGKESGANGASTAPCNQNKPFSVPHTKSLERHIKEELIARGLLESEDRPAEDSKDEVLAKLHK

Parental  RQAELKALSAHNRTKKHDLLRLAKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKKRTPTKKEKDQAWK
          .Q.ELK.LSAHNRTKKH.L.RLAKEEVS.QELRQRV.MADNEVMDAF.KIMAARQKK.TPTKKEKDQAWK
Retrocopy LQTELKVLSAHNRTKKHNLMRLAKEEVSQQELRQRVHMADNEVMDAFWKIMAARQKKQTPTKKEKDQAWK

Parental  TLKERESILKLLDG
          TLKE.ESILKLLDG
Retrocopy TLKEPESILKLLDG

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	0.17 RPM	47.58 RPM
SRP017611_brain	0.08 RPM	47.32 RPM
SRP017611_kidney	0.20 RPM	17.10 RPM
SRP017611_liver	0.07 RPM	14.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2011 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2011 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005324	2 retrocopies	retro_cfam_2011 , retro_cfam_2106,
Equus caballus	ENSECAG00000018186	1 retrocopy	retro_ecab_601,
Mus musculus	ENSMUSG00000048930	2 retrocopies	retro_mmus_1999, retro_mmus_3497,
Otolemur garnettii	ENSOGAG00000034225	1 retrocopy	retro_ogar_362,
Rattus norvegicus	ENSRNOG00000008597	2 retrocopies	retro_rnor_1273, retro_rnor_1479,