RetrogeneDB ID: retro_cfam_945

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:68401084..68401507(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EGFL7
• Ensembl ID: ENSCAFG00000019575
• Aliases: None
• Description: EGF-like-domain, multiple 7 [Source:HGNC Symbol;Acc:20594]

Sequence

>retro_cfam_945
AGGACTGCCTACCGCCCTGGCTGGAAGAGAACCAGCAGGCTCCCCAGGGCCCGTGGAGCAGCAATATGCCAGCCACCATG
CCAGAATGGAGGGAGCTATGTCTAGCCAGGCTGCTGTCACCACCCTGCAGGATGGCAGGGTGACACCTGCCAGACAGACG
TGGATGAATGTGGTGCTGGAGGGGGCACTTGTCCCCCGTACTGTGTGAACACCTCGAATAGTTACTGGTGCCAGTGTCGG
GAAGGGTATAGCCCATCTGCTGATGCTATGCTCTGTCTGCCCAAGTGAAGGACCCCCAGGGTAGCCCCAAACCCTCTGAC
AGGAATGGACAGTACAGTAGAGGAGGAGGTGCAGAGGCTTTGGCCAAGAGTGGATGTGCTGGAGCAGAAGCTGAGTCCCT
TGAGGGCCCTGGAGCACAGGCTG

Alignment

ORF - retro_cfam_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 51.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYACCPGWKRTSGHPMACGAAICQPPCQNGGSCVQPGRCHCPAGWQGNTCQTDVDECSAGGSSCPQCCVN
          R.A..PGWKRTS..P.A.GAAICQPPCQNGGS.V.PG.CH.PAGWQG.TCQTDVDEC.AGG..CP..CVN
Retrocopy RTAYRPGWKRTSRLPRARGAAICQPPCQNGGSYV*PGCCHHPAGWQGDTCQTDVDECGAGGGTCPPYCVN

Parental  TAGSYWCQCREGHNPSTDGVLCLPERGTPRVAPNPTAGVDTAVEEEVQRLRSRVDVLEQKLQLVLAPLHS
          T..SYWCQCREG..PS.D..LCLP...TPRVAPNP..G.D..VEEEVQRL..RVDVLEQKL....A..H.
Retrocopy TSNSYWCQCREGYSPSADAMLCLPK*RTPRVAPNPLTGMDSTVEEEVQRLWPRVDVLEQKLSPLRALEHR

Parental  M
          .
Retrocopy L

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	30.91 RPM
SRP017611_brain	0.08 RPM	27.07 RPM
SRP017611_kidney	0.00 RPM	52.43 RPM
SRP017611_liver	0.00 RPM	34.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_945 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_945 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
Ailuropoda melanoleuca	ENSAMEG00000003952	1 retrocopy	retro_amel_1056,
Canis familiaris	ENSCAFG00000019575	1 retrocopy	retro_cfam_945 ,
Mustela putorius furo	ENSMPUG00000011294	1 retrocopy	retro_mputfur_329,
Mus musculus	ENSMUSG00000026921	1 retrocopy	retro_mmus_1736,
Rattus norvegicus	ENSRNOG00000019388	1 retrocopy	retro_rnor_1362,