RetrogeneDB ID: retro_cfam_2114

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:97958834..97960258(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018651
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000029395
• Aliases: None
• Description: None

Sequence

>retro_cfam_2114
ATGACTTCCATCTTGACTTACACATTTAAAAATCTTCCTAATGCATCAAAATGGGCCCTCCGATTTTCTGTAAGACCTCT
GAGCTGTTCCTCCCAGCTACGAGCTGCCCAGCTGCACAGACCAAATCAAAGAAAACCTTAGCCAAACCCAACATAAGGAA
TATTGTGGTAGTGGATGGTGTTCGCATTCCGTTTTTGCAGTCAGGCACTTCATATAAGGACCTGATGCCACATGATTTGG
CTAGAGCAGCATTTTCGGGTTTGTTGCACCGGACCAATGTCTCAAAGGATGTTGTTGATTATATCATCTTTGGCACAGTT
ATACAGGAAGTGAAAACTAGCAATGTGGCTAGAGAGGCTGCCCTTGGAGCTGGCTTCTCTGATAAGACTCCTGCTCACAC
TGTCACCATGGCCTGCATCTCTGCCAACCAAGCCATGATCACAGGTGTTGGCTTGATCGCTTCTGGGCAGTGTGATGTGG
TTGTGGCAGGTGGTGTAGAGTTAATGTCTGATGTCCCTATTCGTCATTCAAGGAAAATTAGGAAAATGATGCTTGATCTC
AATAAGGCCAAGACTCTGGGTCAACGACTATCTTTACTCTCAAAATTCAGATTGAATTTCCTGTCACCTGAGCTCCCTGC
CGTGGCTGAGTTCTCCACCAGTGAGACCATGGGCCACTCTGCAGACCGGCTAGCCGCTGCTTTTGCTGTTTCTCGAGCGG
ACCAGGATGAGTATGCACTGCGCTCGCACAGCCTTGCCAAGAAGGCACAGGATGAAGGACTCCTGTCTGATATTGTACCC
TTCAAAGTACCAGGAAAAGATACAGTTACCAAAGATAATGACATTCGTCCTTCTTCTCTGGAGCAAATGGCCAAACTAAA
ACCTGCATTCATCAAGCCCTATGGCACGGTGACAACTGCAAATTCTTCTTTCCTGACCGATGGTGCATCTGCAATGCTGA
TTATGGCAGAGGAAAAAGCTCTGGCCATGGGTTATAAGCTCAAGGCGTATTTGAGGGATTTTGTATATGTGTCTCAAGAT
CCAAAAGATCAACTTTTACTTGGACCAACATATGCCACTCCAAAAGTTCTGGAAAAAGCAGGATTAACACTGAATGATAT
TGATGCTTTTGAATTTCATGAAGCATTCTCAGGTCAGATTTTGGCTAATTTTAAAGCCATGGATTCTGACTGGTTTGCAC
AAAACTACATGGGTAGAAAAACCAAGGTTGGGTCACCTCCTCTGGAGAAGTTTAACAACTGGGGTGGATCGCTGTCCCTG
GGACACCCATTTGGAGCTACTGGCTGCCGGTTGGTTATGGCAGGTGCCAACAGATTACGGAAGGAGGGAGGCCAGTATGG
CTTAGTGGCTGCCTGTGCAGCTGGTGGGCAGGGCCATGCTATGATTGTGGAAGCTTATCCAAAA

Alignment

ORF - retro_cfam_2114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSILTYTFKNLPNASKWALRFSVRPLSCSSQLRAA-PAAQTKSKKTLAKPNIRNIVVVDGVRIPFLQSG
          MTSILTYTFKNLPNASKWALRFSVRPLSCSSQLRAA.PAAQTKSKKTLAKPNIRNIVVVDGVRIPFLQSG
Retrocopy MTSILTYTFKNLPNASKWALRFSVRPLSCSSQLRAA<PAAQTKSKKTLAKPNIRNIVVVDGVRIPFLQSG

Parental  TSYKDLMPHDLARAALSGLLHRTNVPKDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMAC
          TSYKDLMPHDLARAA.SGLLHRTNV.KDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMAC
Retrocopy TSYKDLMPHDLARAAFSGLLHRTNVSKDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMAC

Parental  ISANQAMTTGVGLIASGQCDVVVAGGVELMSDVPIRHSRKMRKMMLDLNKAKTLGQRLSLLSKFRLNFLS
          ISANQAM.TGVGLIASGQCDVVVAGGVELMSDVPIRHSRK.RKMMLDLNKAKTLGQRLSLLSKFRLNFLS
Retrocopy ISANQAMITGVGLIASGQCDVVVAGGVELMSDVPIRHSRKIRKMMLDLNKAKTLGQRLSLLSKFRLNFLS

Parental  PELPAVAEFSTSETMGHSADRLAAAFAVSRADQDEYALRSHSLAKKAQDEGLLSDIVPFKVPGKDTVTKD
          PELPAVAEFSTSETMGHSADRLAAAFAVSRADQDEYALRSHSLAKKAQDEGLLSDIVPFKVPGKDTVTKD
Retrocopy PELPAVAEFSTSETMGHSADRLAAAFAVSRADQDEYALRSHSLAKKAQDEGLLSDIVPFKVPGKDTVTKD

Parental  NGIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFVYVSQDPK
          N.IRPSSLEQMAKLKPAFIKPYGTVT.ANSSFLTDGASAMLIMAEEKALAMGYK.KAYLRDFVYVSQDPK
Retrocopy NDIRPSSLEQMAKLKPAFIKPYGTVTTANSSFLTDGASAMLIMAEEKALAMGYKLKAYLRDFVYVSQDPK

Parental  DQLLLGPTYATPKVLEKAGLTLNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKGSQVGSPPLE
          DQLLLGPTYATPKVLEKAGLTLNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTK...VGSPPLE
Retrocopy DQLLLGPTYATPKVLEKAGLTLNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTK---VGSPPLE

Parental  KFNNWGGSLSLGHPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
          KFNNWGGSLSLGHPFGATGCRLVMA.ANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
Retrocopy KFNNWGGSLSLGHPFGATGCRLVMAGANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK

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	2.86 RPM	29.90 RPM
SRP017611_brain	3.18 RPM	22.07 RPM
SRP017611_kidney	41.34 RPM	326.22 RPM
SRP017611_liver	13.34 RPM	145.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2114 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114 ,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,