RetrogeneDB ID: retro_cfam_173

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:60094960..60095341(+)
• Located in intron of: ENSCAFG00000017252

Retrocopy information

• Ensembl ID: ENSCAFG00000017258
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000013864
• Aliases: None
• Description: None

Sequence

>retro_cfam_173
ATGTCTATTGGTGTGCCGATTAAAGTCCTTCACGAAGCCGAGGGCCACATCGTGACATGTGAGACAAACACTGGCGAGGT
GTATCGTGGGAAGCTCATTGAGGCGGAAGACAACATGAACTGCCAGATGTCCAACATCACAGTCACATACAGAGATGGCC
GAGTGGCACAGCTGGAGCAGGTGTACATCCGTGGCAGCAAGATCCGCTTTCTCATTTTGCCTGACATGCTGAAAAATGTA
CCCATGTTAAAGAGCATGAAAAACAAAAACCAAGGCTCAGGAGCTGGCCGGGGGAAAGCTGCTATTCTGAAAGCTCAAGT
GGCTGCAAGAGGAAGAGGACGTGGAATGGGGCGTGGAAACATCTTCCAGAAGCGGAGATAA

Alignment

ORF - retro_cfam_173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF
          MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF
Retrocopy MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF

Parental  LILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
          LILPDMLKN.PMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
Retrocopy LILPDMLKNVPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR

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	7.43 RPM	14.91 RPM
SRP017611_brain	2.54 RPM	6.51 RPM
SRP017611_kidney	8.72 RPM	16.25 RPM
SRP017611_liver	3.12 RPM	7.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_173 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173 ,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dasypus novemcinctus	ENSDNOG00000018004	1 retrocopy	retro_dnov_2611,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Otolemur garnettii	ENSOGAG00000012708	3 retrocopies	retro_ogar_1209, retro_ogar_2077, retro_ogar_2235,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232,
Ictidomys tridecemlineatus	ENSSTOG00000025674	1 retrocopy	retro_itri_651,
Tarsius syrichta	ENSTSYG00000007649	1 retrocopy	retro_tsyr_1489,
Tursiops truncatus	ENSTTRG00000006022	1 retrocopy	retro_ttru_1240,
Vicugna pacos	ENSVPAG00000000241	2 retrocopies	retro_vpac_338, retro_vpac_348,