RetrogeneDB ID: retro_cfam_2106

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:84567968..84568806(+)
• Located in intron of: None

Retrocopy information

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

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_2106
AGGTTCTGGGCTTCTGTAGAGCCCTACTGTGCTGATATCACCAGTGAGAAAGTATGCACACTAGAGAAACTACTGAAACC
CCCAGAAGATGAGGCTGAACATTACAAGCTCCCACCCCTGAGGAAGCACTACTCCCAACGCTGGGCGCAGCAGGACCTGC
TGGAGGAACAGAAGGATGGGGCCTGGGCAGCAGCCGTGACTGACAAGAAAAAAGGCCTTATGGGGCCATTGAGCCAACTG
CACACTAAAGATCTGGATGCCCTGCTGAAGAAGTCTGAGGCCCAGCATGAGCAGCCTGAAGATGGGTGCCCCTTTGGTGC
TCTGATGCAGCGCCTCCTACAGGCCCTAGTAAAGGAAAATATCACTTCCCCTATGGAGGACTCTCCTATTCCTGACATGT
CTGGGAAGGAATCAGGAGCCGATGGGGCAAGCACCTCTCCCCACAATCAGAACAAGCCCTTCAGTGTGCCACATACCAAG
TCCCTGGAGAGCCGCATCAAGGAGGAGCTGATTGCCCAGGGCCTGCTGGAGTCTGAGGACCGCCCTGCAGAGGACTCAGA
AGATGATATCCTTGCTGAGCTGGCAAACGGCAGGCCGAGCTGAAGGCACTCAGTGCCCATAACCGTGTGGAGAAGCACGA
CATGCTGAGGCTGGGAAAAGGGAGGTAAGCCGGCAGGAGCTGAGGCAGAGGGTCCGCATGGCAGACAGCAAGGTCATGGA
CACCTTCTGGAAGATCATGGCTGCCCGGCAGAAGAAGCGGACCCCAACCAAGAAGGAGAAGGACCAGGCCTGGAAGACTC
GGAAGGAGCGTGAGAGCATCCTAAAGCTGCTGGATGGG

Alignment

ORF - retro_cfam_2106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 64.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RFWASVEPYCADITSEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLEEQKDGARAAAVADKK
          RFWASVEPYCADITSE.V.TLE.LLKPPEDEAEHYK.PPL.KHYSQRWAQ.DLLEEQKDGA.AAAV.DKK
Retrocopy RFWASVEPYCADITSEKVCTLEKLLKPPEDEAEHYKLPPLRKHYSQRWAQQDLLEEQKDGAWAAAVTDKK

Parental  KGLMGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQALVEENIISPMEDSPIPDMSGKESGA
          KGLMGPL..L.TKD.DALLKKSEAQHEQPEDGCPFGAL.QRLLQALV.ENI.SPMEDSPIPDMSGKESGA
Retrocopy KGLMGPLSQLHTKDLDALLKKSEAQHEQPEDGCPFGALMQRLLQALVKENITSPMEDSPIPDMSGKESGA

Parental  DGASTSPRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELR-KRQAELKALSAHNR
          DGASTSP.NQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSED..LAEL..KRQAELKALSAHNR
Retrocopy DGASTSPHNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDDILAELA<KRQAELKALSAHNR

Parental  TKKHDLLRL-AKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKKRTPTKKEKDQAWKTLKERESILKLL
          ..KHD.LRL..K.EVSRQELRQRVRMAD..VMD.F.KIMAARQKKRTPTKKEKDQAWKT.KERESILKLL
Retrocopy VEKHDMLRL<GKREVSRQELRQRVRMADSKVMDTFWKIMAARQKKRTPTKKEKDQAWKTRKERESILKLL

Parental  DG
          DG
Retrocopy DG

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	0.34 RPM	47.58 RPM
SRP017611_brain	0.00 RPM	47.32 RPM
SRP017611_kidney	0.07 RPM	17.10 RPM
SRP017611_liver	0.00 RPM	14.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2106 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2106 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,