RetrogeneDB ID: retro_cfam_1255

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:45752878..45753614(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNS1
• Ensembl ID: ENSCAFG00000016053
• Aliases: None
• Description: meiosis-specific nuclear structural 1 [Source:HGNC Symbol;Acc:29636]

Sequence

>retro_cfam_1255
ATGGCTTCTAGAAGGTAAACTTTGAGCTTCAGTGAAAGGCATCAGAAATCAGTAGATATAAATCACTGCAAACAATTGTA
ATCACTAAGAAAGATATAGAATAATGTCAGGGGCCAGGTGATGCAGAATGAAAATAATGACTGCGTGGAGCACAAAGATT
CCTCAGATTATTACAGAATGAACAATTTGAGTTGGATATGGAAGAGGCCATTCAAAAGGCAGAAGAAAACAAAAGACTGA
GGAACTCCAGCTTGAACAAGAAGAAAAATTGGTTATGAAATTGGCAAAACTAAAACATGATAGTCTAACAGATAAAAAGA
TGAGGCGACAAGTAAGAGAAAACAGTATTAAGCTCAGAGAATTGAAGAAAAAATTAAAAGCAGCTTACATGAATAAAGAA
AGGGCAGCTCAGATTGCAGAGAAGGATACCATTAAATATGAGCAAATGAAACAGTGTGCTGAAATAGCCAAAACCATGAT
GGAATAACATAAGAGAACAATAAAGGAAGAGACTGCTGCAGAGGACAAAAGAAATAAAGTAAAAACACGGTATTATCTGG
CCTTAGAGAAACAACTTGAAGAACAAGAAAAGAGAAAGCAGGAAGTGTATGAGCAGTTCCTGAAAGAGACACTCATGATT
GATGAAATTGTTTGGAAAATCTATGAAGAAGATCAATTGGAAAGACAACAAAAGTTAGACAAAATGAATGTAACTCAAAG
GTACATAGAAGAGTTT

Alignment

ORF - retro_cfam_1255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 50.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRRRALSFSERHQKLVDVNYGKQLHVQSLRKIENTIKDQVVHHENDDRVERK-RFLRLLQNEQFELDM
          MASRR..LSFSERHQK.VD.N..KQL...SLRKI.N....QV...EN.D.VE.K.RFLRLLQNEQFELDM
Retrocopy MASRR*TLSFSERHQKSVDINHCKQL*--SLRKI*NNVRGQVMQNENNDCVEHK<RFLRLLQNEQFELDM

Parental  EEAIQKAEENKRLR-ELQLEQEEKLAMELAKLKHESLKDEKMRQQVRENSIELRELEKKLKAAYMNKERA
          EEAIQKAEENKRLR.ELQLEQEEKL.M.LAKLKH.SL.D.KMR.QVRENSI.LREL.KKLKAAYMNKERA
Retrocopy EEAIQKAEENKRLR<ELQLEQEEKLVMKLAKLKHDSLTDKKMRRQVRENSIKLRELKKKLKAAYMNKERA

Parental  AQIAEKDAIKYEQMKRDAEIAKTMMEEHERVIKEESAAEDKRNKVKAQYYLDLEKQLEEQEKKKQEAYEQ
          AQIAEKD.IKYEQMK..AEIAKTMME.H.R.IKEE.AAEDKRNKVK..YYL.LEKQLEEQEK.KQE.YEQ
Retrocopy AQIAEKDTIKYEQMKQCAEIAKTMME*HKRTIKEETAAEDKRNKVKTRYYLALEKQLEEQEKRKQEVYEQ

Parental  LLKEKLMIDEIVRKIYEEDQLERQQKLEKMNVTRRYIEEF
          .LKE.LMIDEIV.KIYEEDQLERQQKL.KMNVT.RYIEEF
Retrocopy FLKETLMIDEIVWKIYEEDQLERQQKLDKMNVTQRYIEEF

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	0.04 RPM	5.29 RPM
SRP017611_brain	0.00 RPM	2.46 RPM
SRP017611_kidney	0.00 RPM	7.40 RPM
SRP017611_liver	0.00 RPM	0.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1255 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1255 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016053	1 retrocopy	retro_cfam_1255 ,
Tupaia belangeri	ENSTBEG00000004372	3 retrocopies	retro_tbel_1821, retro_tbel_2477, retro_tbel_2534,