RetrogeneDB ID: retro_cfam_941

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:55907892..55908469(-)
• Located in intron of: ENSCAFG00000008180

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005385
• Aliases: None
• Description: None

Sequence

>retro_cfam_941
CCAGAGCTGGAGCCCCAGCCGCAGGAAGAAGCCATGCAGCTGAGCTGGGAGAAGCGGTGGCGTCCCCCATGGATGACGCG
TTCCTGAGCCTGGACTCGCCCACCTATGTCCTGTACAGGCCCAGAACAGAATGGGCTGATAGAGATACAGTGCTGCAGAA
CGATGGCCCCAATCCAGGGGTCCGGATCATTTATAGTGAAAAATTTAGAGACGTGTATGATTATTTCCGGATCATTCTGC
AGTGTGATGAAAGAAGTGAACGAGCTTTTAAAGTCAGCAGAGATGCTACTGAGTTAAATGCAGCCAATTATACAGTGTGG
CATTTTCGGAAAGTTCTCTTGAAGTCACTTCAAAATCATCTAAATGAAGAAATGAACTACATCACTGCAGTAATTGAGAA
ACAGCCCCAAAACTATCAAGTTTGGCATCAGAGGCGAGTATTAATGGAATGGCTACAAGATCCATCTCAGGAGCTTGAGT
TTATTGCTGATATTCTTATCAGAATGCAAAGAATTACCAAGCCTGGCAACATCGACAATGGGTTATCCAGGAATTTAAAC
TTTGGGATAATAAGCTG

Alignment

ORF - retro_cfam_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 50.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPLQPQQQEEAM-AAELGEAVASPMDDGFLSLDSPTYVLYRDRAEWADIDPVPQNDGPNPVVQIIYSEKF
          P.L.PQ.QEEAM.AAELGEAVASPMDD.FLSLDSPTYVLYR.R.EWAD.D.V.QNDGPNP.V.IIYSEKF
Retrocopy PELEPQPQEEAM<AAELGEAVASPMDDAFLSLDSPTYVLYRPRTEWADRDTVLQNDGPNPGVRIIYSEKF

Parental  RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNY
          RDVYDYFR..LQ.DERSERAFK..RDA.ELNAANYTVWHFR.VLLKSLQ..L.EEMNYITA.IE.QP.NY
Retrocopy RDVYDYFRIILQCDERSERAFKVSRDATELNAANYTVWHFRKVLLKSLQNHLNEEMNYITAVIEKQPQNY

Parental  QVWHHRRVLVEWLKDPSQELEFIADIL-NQDAKNYHAWQHRQWVIQEFKLWDNEL
          QVWH.RRVL.EWL.DPSQELEFIADIL..Q.AKNY.AWQHRQWVIQEFKLWDN.L
Retrocopy QVWHQRRVLMEWLQDPSQELEFIADIL<YQNAKNYQAWQHRQWVIQEFKLWDNKL

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	49.05 RPM
SRP017611_brain	0.00 RPM	44.94 RPM
SRP017611_kidney	0.00 RPM	116.69 RPM
SRP017611_liver	0.00 RPM	29.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_941 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_941 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003201	2 retrocopies	retro_btau_1431, retro_btau_1768,
Canis familiaris	ENSCAFG00000005385	1 retrocopy	retro_cfam_941 ,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Macaca mulatta	ENSMMUG00000017158	1 retrocopy	retro_mmul_1078,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Pteropus vampyrus	ENSPVAG00000013502	2 retrocopies	retro_pvam_1157, retro_pvam_1433,
Tursiops truncatus	ENSTTRG00000008870	1 retrocopy	retro_ttru_579,