RetrogeneDB ID: retro_cfam_466

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:48093842..48094630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GCM1
• Ensembl ID: ENSCAFG00000002273
• Aliases: None
• Description: glial cells missing homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:4197]

Sequence

>retro_cfam_466
AATGTCAAAAAGACCGACTGGTTCCAGGAATGGCCAGATTCTTATGAGAAGCACATCTACAGCTCTGAGGACAGGACTGC
ACAACGGCATCTGAGCAGCTGGGCCATGTGCAACACCAACAACCACAACTCCCGCGTCCTCAAGAAGTCCTGCCTGGGTG
TGGTGGTGTGCAGCCGCGACTGCTCCGCCGAGGAGGGCCGCAAGACGTACCTGAGACCTGCCATCTGTGACAAAGCCCGG
CAGAAGCAGCAGAGGAAACGCTGCCCTAATTGTGATGGGCCTCTGAAGCTGATTCCTTGCCGAGGCCATGGGGGCTTCCG
GTCACCAACTTCTGGAGGCACGAGGGATGCTTCATATTCTTCCAGTCAAAAGGAGAGCACGATCATCCAAAACCAGAAAC
TAAATTGGAAGCCGAGGCAAGAAGAACAACGAAGAAAGCACACACAGCATCTTCCTCTGTCTCCTTAAAGCTGAAGGGGC
GCCCAGAGACAAAGTCTCTTTCAGGTGAAACTCAAAGTTGGGGAAGTTTACCTTTAACTTGGTCTTTCCAGGAAGGCGTC
CAATTGCCTGGTAGTTACAGTGGACCTTTAATAGCTAAGCCTCCCCAGCAGAAGTCACTGAATGATTGCTTATTCTTCTC
CAAGACTTATTGTTTGGGGGGAACCACTCATTTGGCAGACCCCACTTCCACCTTGGGCCCCACTAAGCTCTATGAGAAAT
GCAAACTGTCCAGTAGTTGGATCTATAAGAGTGGGGACCTGCTTCATCCTGTTTCTGGAGTCTTCTCT

Alignment

ORF - retro_cfam_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 60.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVKKTDWFQEWPDSYEKHIYSSEDRNAQRHLSSWAMRNTNNHNSRILKKSCLGVVVCSRDCSAEEGRKIY
          NVKKTDWFQEWPDSYEKHIYSSEDR.AQRHLSSWAM.NTNNHNSR.LKKSCLGVVVCSRDCSAEEGRK.Y
Retrocopy NVKKTDWFQEWPDSYEKHIYSSEDRTAQRHLSSWAMCNTNNHNSRVLKKSCLGVVVCSRDCSAEEGRKTY

Parental  LRPAICDKARQKQQRKRCPNCDGPLKLIPCRGHGGF-PVTNFWRHDGRFIFFQSKGEHDHPKPETKLEAE
          LRPAICDKARQKQQRKRCPNCDGPLKLIPCRGHGGF.PVTNFWRH.G.FIFFQSKGEHDHPKPETKLEAE
Retrocopy LRPAICDKARQKQQRKRCPNCDGPLKLIPCRGHGGF<PVTNFWRHEGCFIFFQSKGEHDHPKPETKLEAE

Parental  ARRTMKKAHTASSSVSLKLKGSPETKSLSGETQSWGSLPLTWSFQEGVQLPGSYSGRLIAKPPQQKSLND
          ARRT.KKAHTASSSVSLKLKG.PETKSLSGETQSWGSLPLTWSFQEGVQLPGSYSG.LIAKPPQQKSLND
Retrocopy ARRTTKKAHTASSSVSLKLKGRPETKSLSGETQSWGSLPLTWSFQEGVQLPGSYSGPLIAKPPQQKSLND

Parental  CLFFSKTYCLGGTTDLADPTSTLGPTKLYEKCKLSSSWIYNSGDLLHPVSGVFS
          CLFFSKTYCLGGTT.LADPTSTLGPTKLYEKCKLSSSWIY.SGDLLHPVSGVFS
Retrocopy CLFFSKTYCLGGTTHLADPTSTLGPTKLYEKCKLSSSWIYKSGDLLHPVSGVFS

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	15.78 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_466 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002273	1 retrocopy	retro_cfam_466 ,
Rattus norvegicus	ENSRNOG00000007932	1 retrocopy	retro_rnor_2476,
Ictidomys tridecemlineatus	ENSSTOG00000014763	1 retrocopy	retro_itri_77,