RetrogeneDB ID: retro_cfam_1684

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:17145310..17145992(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSCAFG00000019045
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_cfam_1684
CCCCAGGCCCCCATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCCTGGGACCCAGCGGTTGCAGCCCAATTCTATGGA
TCCCACCCGACAACAAGGGCACCCCAACCTGGGAGGATCGATGAGAGAATGAACCCTCCCCGAGGCATGGGGCCCATGGG
GCCTGGCCCACAGCATTACGGCAGCGGCATGAGACCACCACGCAACTCCCTCGGCCCGCCATGCCCGGGGGTGACATGGG
CCCGGGAGCTGGCAGGCCCTGGCCAGATCCCAACAGTGCTAACTCAACTCCTTACTCCTCCTCATCACCTGGTACCTACG
TGGGACCTCCTGGTGGTGGCCCCCCAGGAACACCCATCATGCTTAGTCCTGCAGATTTAACAAATTCCAGTGACAGCATC
TACACCATGATTAATCCGGTGCCGCCTGGAGGCAGCCGGTCCAACTTCCCCATGGGTCCAGGCTCGCACGGCCGGATGGA
AGGCATGGGCGGCATGGAGCCACACCACATGAACGGATCGTTAGGGTCAGGTGACATAGATGGACTTCCCAAAAATTCTT
CTAACAACATAAGTGGCATTAGCAATCCTCCAGGCACCCCTTGAGACGATGGCGATCTAGGAGAGAACTTCCTCCACTCC
TTCCAGAATGACAATTTTTCTCCAAGCATGAGGATGAGCATG

Alignment

ORF - retro_cfam_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 82.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSSMMGPHSQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSM-QRMNPPRGMGPMGPGPQNYGSGMRPPPN
          P........QPPGGVPGTQ.L.PNSMDPTRQQGHPN.GGSM..RMNPPRGMGPMGPGPQ.YGSGMRPP.N
Retrocopy PQAPIRMGNQPPGGVPGTQRLQPNSMDPTRQQGHPNLGGSM<ERMNPPRGMGPMGPGPQHYGSGMRPPRN

Parental  SLGP-AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVGPPGGGGPPGTPIMPSPADSTNSSDNIYTM
          SLGP.AMPG..MGPGAGRPWP.PNSANS.PYSSSSPGTYVGPPGGG.PPGTPIM.SPAD.TNSSD.IYTM
Retrocopy SLGP<AMPGGDMGPGAGRPWPDPNSANSTPYSSSSPGTYVGPPGGG-PPGTPIMLSPADLTNSSDSIYTM

Parental  INPVPPGGSRSNFPMGPGSDGPMGGMGGMEPHHMNGSLGSGDIDGLPKNSPNNISGISNPPGTPRDDGEL
          INPVPPGGSRSNFPMGPGS.G.M.GMGGMEPHHMNGSLGSGDIDGLPKNS.NNISGISNPPGTP.DDG.L
Retrocopy INPVPPGGSRSNFPMGPGSHGRMEGMGGMEPHHMNGSLGSGDIDGLPKNSSNNISGISNPPGTP*DDGDL

Parental  GGNFLHSFQNDNYSPSMTMSV
          G.NFLHSFQNDN.SPSM.MS.
Retrocopy GENFLHSFQNDNFSPSMRMSM

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	0.04 RPM	169.42 RPM
SRP017611_brain	0.24 RPM	139.97 RPM
SRP017611_kidney	0.00 RPM	25.09 RPM
SRP017611_liver	0.00 RPM	12.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1684 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019045	1 retrocopy	retro_cfam_1684 ,
Echinops telfairi	ENSETEG00000000453	1 retrocopy	retro_etel_1455,