RetrogeneDB ID: retro_cfam_1337

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:28098468..28099557(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CPNE1
• Ensembl ID: ENSCAFG00000031721
• Aliases: None
• Description: Canis lupus familiaris copine I (CPNE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001171749]

Sequence

>retro_cfam_1337
ATGGCCCACTGTGTGACCTTGGTTCATCTATCCATTTCCTGTGACCACCTCATTGACAAGGACATCGCCTCCAAGTCTGA
CCCACTCTGTGTCCTTTTACAGGATGTGGGAGAGGGCAGCTGGGCTGAGCTTGGCTGAACTGAGCAAGTGCGGAACTGCT
CAAGCCCTGAGTTCTCCAAGACTCTGCAGCTTGAGTACCACTTTGAAACAGTCCAGAAGCTCCTATTTGGCATCTATGAC
ATAGACAACAAGACACCTGAGCTGGGGGATGATGACTTCCTAGGAAGGGCTGAGTGTTCCCTAGGACAGATTGTGTCCAG
CCACATAATAACTCTACCCTTGATGCTGAAGCCTGGAAAACCTGCTGGGCGGGGGACCATCACAGTATCTGCTCAAGAGA
TGAAGGATAGTCATGTAGTGACCATGGAGGTGGAGGCCAGAAATCTAGATAAGAAGGACTTCCTGGGGAAATCAGATCCA
TTCTTGGAGTTCTTCCGTCAGGGTGATGGGAAATGGCACCTGGCCTACAGATCTGCGGTAATCAAGAACAACTTGAACCC
TACATGGAAGCACTTCTCTGTTCCCCTTCAGCACTTCCGTGGGGGGAGACCCCAGCACACCCATCCAGGTGCGATGCTCC
GATTATGACAGTGATGGTTCACACGATCTCATTGGTACCTTCTACACCAGCTTGGCCCAACTGCAAGCAGCCCCGGCTGA
GTTTGAATGCATCCACCCTGAGAAACAGCAGACAAAGAAAAGCTACAAGAATCTGGGGCTGTTCTTGTCAAGATTTGCCA
GGTAGAAACACAATATTCATTCCCGGACTATGTGATGGGAGGCTGTCAAATCAACTTCACTGTAGGCATGGACTTCACAG
GCTCTAATGGAGACCCTTCCTCCCCAGACTCTCTGCACTACCTGAGCCCAATAGGGGTCAATGAATACCTGATAGCACTG
TGGAGTGTGGGCAGCGTGATCCAGGACTATGACTCGGAGAAGCTGTTCCCAGCATTTGGATTTGGGGCCCAGGTACCTCC
TGATTGGCAGGTCTCCCATGAATTTGCCTTGAACTTCAGCCCCAGTAAC

Alignment

ORF - retro_cfam_1337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.25 %
• Parental protein coverage: 67.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAHCVTLVQLSISCDHLIDKDIASKSDPLCVLLQDVGGGSWAELGRTERVRNCSSPEFSKTLQLEYHFET
          MAHCVTLV.LSISCDHLIDKDIASKSDPLCVLLQDVG.GSWAELG.TE.VRNCSSPEFSKTLQLEYHFET
Retrocopy MAHCVTLVHLSISCDHLIDKDIASKSDPLCVLLQDVGEGSWAELG*TEQVRNCSSPEFSKTLQLEYHFET

Parental  VQKLRFGIYDIDNKTPELGDDDFLGGAECSLGQIVSSHIITLPLMLKPGKPAGRGTITVSAQEMKDSHVV
          VQKL.FGIYDIDNKTPELGDDDFLG.AECSLGQIVSSHIITLPLMLKPGKPAGRGTITVSAQEMKDSHVV
Retrocopy VQKLLFGIYDIDNKTPELGDDDFLGRAECSLGQIVSSHIITLPLMLKPGKPAGRGTITVSAQEMKDSHVV

Parental  TMEVEARNLDKKDFLGKSDPFLEFFRQGDGKWHLAYRSEVIKNNLNPTWKRFSVPLQHF-CGGDPSTPIQ
          TMEVEARNLDKKDFLGKSDPFLEFFRQGDGKWHLAYRS.VIKNNLNPTWK.FSVPLQHF..GGDPSTPIQ
Retrocopy TMEVEARNLDKKDFLGKSDPFLEFFRQGDGKWHLAYRSAVIKNNLNPTWKHFSVPLQHF>VGGDPSTPIQ

Parental  VRCSDYDSDGSHDLIGTFYTSLAQLQAVPVEFECIHPEKQQKKKSYKN-SGTVRVKICQVETQYSFLDYV
          VRCSDYDSDGSHDLIGTFYTSLAQLQA.P.EFECIHPEKQQ.KKSYKN.SG.V.VKICQVETQYSF.DYV
Retrocopy VRCSDYDSDGSHDLIGTFYTSLAQLQAAPAEFECIHPEKQQTKKSYKN<SGAVLVKICQVETQYSFPDYV

Parental  MGGCQINFTVGMDFTGSNGDPSSPDSLHYLSPSGVNEYLTALWSVGSVIQDYDSDKLFPAFGFGAQVPPD
          MGGCQINFTVGMDFTGSNGDPSSPDSLHYLSP.GVNEYL.ALWSVGSVIQDYDS.KLFPAFGFGAQVPPD
Retrocopy MGGCQINFTVGMDFTGSNGDPSSPDSLHYLSPIGVNEYLIALWSVGSVIQDYDSEKLFPAFGFGAQVPPD

Parental  WQVSHEFALNFNPSN
          WQVSHEFALNF.PSN
Retrocopy WQVSHEFALNFSPSN

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	0.08 RPM	26.75 RPM
SRP017611_brain	0.24 RPM	25.25 RPM
SRP017611_kidney	0.07 RPM	43.25 RPM
SRP017611_liver	0.00 RPM	21.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1337 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031721	1 retrocopy	retro_cfam_1337 ,