RetrogeneDB ID: retro_cfam_33

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:14142657..14143263(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009878
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000016482
• Aliases: None
• Description: None

Sequence

>retro_cfam_33
ATGGCCAAGGTTTCTGTGCTGAACGTGGCGGTGCTGGAGAATCCGAGCCCTTTCCACAGCCCCTTCCGGTTCGAGATCAG
CTTTGAGTGCAATGAGGCCCTGGCGGACGATCTAGAATGGAAGATCATTTATGTTGGCTCAGCTGAGAGTGAGGAGTTTG
ACCAAATCCTGGACTCTGTGCTAGTTGGCCCTGTCCCAGCAGGGAGGCACATGTTCATCTTTCAGGCTGATGTCCCCAAC
CCATCCCTCATCCCAGAGACTGATGCTGTGGGTGTGACCGTGGTCCTCATCACCTGCACCTACCATGGACAGGAGTTCAT
CCGTGTGGACTACTACGTCAACAATGAATACCCCAATCCCGAGCTGAGGGAGAACCCACCCCTGAAGCCAGACTTCTCTC
AGCTCCAGAGGAACATCTTGGCCTCAAACCCCCGAGTGACCCGCTTCCACATCAACTGGGACAACATGGACAGACTAGAG
GCCATAGAGAACCAGGACCCCACCCTGGGCTGTGGCCTCCCCTTCAGCTGTGCTCCCATCAAAGGCTTGGGTCTCCCAGG
TTGCATTCCTGGGCTCCTACCCGAGAATTCCATGGACTGCATCTAA

Alignment

ORF - retro_cfam_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKVSVLNVAVLENPSPFHSPFRFEISFECNEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRH
          MAKVSVLNVAVLENPSPFHSPFRFEISFECNEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRH
Retrocopy MAKVSVLNVAVLENPSPFHSPFRFEISFECNEALADDLEWKIIYVGSAESEEFDQILDSVLVGPVPAGRH

Parental  MFIFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYPNPELRENPPLKPDFSQLQRNIL
          MFIFQAD.PNPSLIPETDAVGVTVVLITCTYHGQEFIRV.YYVNNEYPNPELRENPPLKPDFSQLQRNIL
Retrocopy MFIFQADVPNPSLIPETDAVGVTVVLITCTYHGQEFIRVDYYVNNEYPNPELRENPPLKPDFSQLQRNIL

Parental  ASNPRVTRFHINWDNMDRLEAIENQDPTLGCGLPFSCAPIKGLGLPGCIPGLLPENSMDCI
          ASNPRVTRFHINWDNMDRLEAIENQDPTLGCGLPFSCAPIKGLGLPGCIPGLLPENSMDCI
Retrocopy ASNPRVTRFHINWDNMDRLEAIENQDPTLGCGLPFSCAPIKGLGLPGCIPGLLPENSMDCI

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	0.76 RPM
SRP017611_brain	0.00 RPM	0.08 RPM
SRP017611_kidney	0.07 RPM	0.86 RPM
SRP017611_liver	0.00 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_33 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_33 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004085	1 retrocopy	retro_btau_662,
Canis familiaris	ENSCAFG00000016482	1 retrocopy	retro_cfam_33 ,
Echinops telfairi	ENSETEG00000013713	1 retrocopy	retro_etel_379,
Myotis lucifugus	ENSMLUG00000000537	4 retrocopies	retro_mluc_1426, retro_mluc_2042, retro_mluc_2614, retro_mluc_775,
Monodelphis domestica	ENSMODG00000012099	4 retrocopies	retro_mdom_366, retro_mdom_367, retro_mdom_369, retro_mdom_688,
Sorex araneus	ENSSARG00000000534	1 retrocopy	retro_sara_552,