RetrogeneDB ID: retro_cfam_1539

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:502304..502657(+)
• Located in intron of: ENSCAFG00000009159

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3BGRL3
• Ensembl ID: ENSCAFG00000012567
• Aliases: None
• Description: SH3 domain binding glutamic acid-rich protein like 3 [Source:HGNC Symbol;Acc:15568]

Sequence

>retro_cfam_1539
TCTGGGTCTCCAGGCCGTGCAGCTGCCGCTACCACCGACCGTCCGCCTGTCGGCCCGCTCATCCACCCGCAGCATGAGTG
GCCTGCGCGTCTACGAGCACGTCGGTCACCGGCTCCTGTGAGATCAAGTCCTAGCAGAGCGAGGTGACCCGCATCCTGGA
TGGGAAGCGCATCCAGTACCAGCTAGTGGACATCTCCCAGGACAACGCCCTGCGGGATGAGATGCGAGCCTTGGCGGGCA
ACCCCAAGGCCACCCCACCCCAGATTGTCAACGGGGACCAGTACTGTGGGGACTATGAGCTCTTCGTGGAGGCTGTGGAA
CAAAACACACTGCAGGAGTTCCTGAAATTGGCC

Alignment

ORF - retro_cfam_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASSPCRAA-AAT-AVRPPARSSTRSMSGLRVY-STSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDN
          ..SP.RAA.A.T..VR..ARSSTRSMSGLRVY.STSVTGS.EIKS.QSEVTRILDGKRIQYQLVDISQDN
Retrocopy SGSPGRAAAATT>TVRLSARSSTRSMSGLRVY>STSVTGSCEIKS*QSEVTRILDGKRIQYQLVDISQDN

Parental  ALRDEMRALAGNPKATPPQIVNGDQYCGDYELFVEAVEQNTLQEFLKLA
          ALRDEMRALAGNPKATPPQIVNGDQYCGDYELFVEAVEQNTLQEFLKLA
Retrocopy ALRDEMRALAGNPKATPPQIVNGDQYCGDYELFVEAVEQNTLQEFLKLA

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	36.12 RPM
SRP017611_brain	0.32 RPM	40.97 RPM
SRP017611_kidney	0.00 RPM	28.86 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1539 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1539 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012567	1 retrocopy	retro_cfam_1539 ,
Homo sapiens	ENSG00000142669	1 retrocopy	retro_hsap_3470,
Macropus eugenii	ENSMEUG00000007201	1 retrocopy	retro_meug_388,
Nomascus leucogenys	ENSNLEG00000009265	1 retrocopy	retro_nleu_341,
Pan troglodytes	ENSPTRG00000000379	1 retrocopy	retro_ptro_2353,