RetrogeneDB ID: retro_cfam_849

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:22273543..22274532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSCAFG00000015607
• Aliases: None
• Description: transcriptional adaptor 1 [Source:HGNC Symbol;Acc:30631]

Sequence

>retro_cfam_849
GCGGCCTCTGTGAGCGAGCTGGAAGCGGCCAAGAAGAACTTGGGCGAGGCCCTGGGGGACAACGTGAAACAACACTGGGC
TAAGTTAAAGTTGTGGTTCAAGCAGAAGATCAGCAAAGAAGAGTTTGACCTTGAAGCCCATAGACTTCTCACGCAGGATA
ATGTCCATTCTCACAACGACTTCCTCCTGGCTATTCTTACGCGTTGTCAGATTTTGGTGTCTACACCAGAGGGTGCTGGA
TCTTTGCCCTGGACCGGGGGTTCTGCAGCTAACCCTGGAAAACCAAAGGGAAGGAAAAAACTTTCTTCTGTTCGTCAGAA
ATTTGATCATAGATTCCAGCCTCAAAATCCCCTCTCGGGAGCCCAGCTTGTGGCAAAGGATCCCCAAGATGATGATGACT
TGAAACTTTGTTCCCACACAATGATGCTTCCCACTCGGGGTCAGCTGGAAGGGAGGATGATAGTGACTGCTTAGGAGCAG
GGGTTGGACAACGTCACCGAGGAGGCAGTCTCAGCTGTTGTCTATGCGGTGGAGAATCACCTTACAGATATATTGACATC
AGCTGTGTCAAGAAGGCAAGCTTATCGGTCACATGCTGGCCACTTTAAGTATGCCTTGGGTAGTAACGTAACCCGCAGCC
ATCCCTGAAGAGTGGTGTAGTCGCTTACAACAGCGTAAGGGCAAGCCCTCGGCCTCTGCTCCTATGCAGGTCAGAACCCA
GCTTCCCACCGCCCCCCCGATGGCGCGGAGCAGCAAGCTGCACGCCTGGCGTGCTCTGGGGCTACCGTCCCTGCGTCTTT
GCCTCCGGCCAACATGCACGACCTTTGTGACCTTTGCAGGTACACAGGGAAGTCATTCCTACACACACTGTATACGCTCT
CAACGTTGAAAGGATCATCATGAAACTCTGGCATCCAAACCATGAAGAGCTGCAGCAAGACAAAGTCCACCGCCAGCGCC
TGGCAGCCAAGGAAGGGCTTTTGCTCTGC

Alignment

ORF - retro_cfam_849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.5 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ATFVSELEAAKKNLSEALGDNVKQYWANLKLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTRCQ
          A..VSELEAAKKNL.EALGDNVKQ.WA.LKLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTRCQ
Retrocopy AASVSELEAAKKNLGEALGDNVKQHWAKLKLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTRCQ

Parental  ILVSTPEGAGSLHWTGGSAAKPGKPKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKLCSH
          ILVSTPEGAGSL.WTGGSAA.PGKPKG.KKLSSVRQKFDHRFQPQNPLSGAQ..VAKDPQDDDDLKLCSH
Retrocopy ILVSTPEGAGSLPWTGGSAANPGKPKGRKKLSSVRQKFDHRFQPQNPLSGAQ-LVAKDPQDDDDLKLCSH

Parental  TMMLPTRGQLEGRMIVTAYEHGLDNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAFGSN
          TMMLPTRGQLEGRMIVTA.E.GLDNVTEEAVSAVVYAVENHL.DILTS.VSRR.AYR...GHFKYA.GSN
Retrocopy TMMLPTRGQLEGRMIVTA*EQGLDNVTEEAVSAVVYAVENHLTDILTSAVSRRQAYRSHAGHFKYALGSN

Parental  VT-PQPYLKNSVVAYNNLIESPP-AFSAPC-AGQNPASHPPPDDAEQQAALLLACSGDTLPASLPPVNMY
          VT.PQP.LK.S.V...N.....P...SAP..AGQNPASH.PPD.AEQQAA.L.ACSG.T.PASLPP.NM.
Retrocopy VT<PQPSLK-SGVVAYNSVRASP<SASAPM<AGQNPASHRPPDGAEQQAARL-ACSGATVPASLPPANMH

Parental  DLFEA-LQVHREVIPTHTVYALNIERIIMKLWHPNHEELQQDKVHRQRLAAKEGLLLC
          DL....LQVHREVIPTHTVYALN.ERIIMKLWHPNHEELQQDKVHRQRLAAKEGLLLC
Retrocopy DLCDL<LQVHREVIPTHTVYALNVERIIMKLWHPNHEELQQDKVHRQRLAAKEGLLLC

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	0.00 RPM	16.25 RPM
SRP017611_brain	0.00 RPM	15.32 RPM
SRP017611_kidney	0.00 RPM	10.43 RPM
SRP017611_liver	0.00 RPM	5.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_849 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_849 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849 ,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,