RetrogeneDB ID: retro_cfam_2168

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:59146932..59147674(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGO
• Ensembl ID: ENSCAFG00000002000
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class O [Source:HGNC Symbol;Acc:23215]

Sequence

>retro_cfam_2168
TTATGTATCTTAGACTCTTATAAGACAAGCTACAATTGGAAGACCCTGAGTATGCTATCACACAGCTAGCTCAGAGGACC
ATAAATCAGAGCTTGGAAAACTTTCTCTGGAAAAAGTCTTCTAGGAGTAGGAGTCTCTGAATGCTAGCATTGTGAATAAA
TACCATCATACAAGCTGCTGACTGCTGGGGTATTCACTGCCTCCATTATGAGATCAATGATATCCATGTGCCACTCTAGG
TGAAAGAATCCATGCAGAAGGAGGTAGAGGCAGAGGTGGAAAATGGGCCACAGTTCTAGAGTCTGAGGGGATCCAGGAGT
CATCCAACAATTTGGTAAAGGGGAAGAATCAGGCATAGATCCTGGCCTCCCAGGCAGAAAAGCCAGAACAAATAAATAAG
GCAGCAGGATAGGCCAGTGCTGTTCTGGCCAAGACCAAGGCTAAGGCTAAGATCCTGGCTGCAGTTCTGACACAACATAA
TGGAGATGCAGCAGCGTCACTGACAATGGCTGAGCAGTATTTCAGTGTGTTCTCCAAATTGGTCTAGTATTCCAACACTA
TCCTGCTGCCCTCCAACCCCTGCAATGTCATCACTATGGTGGCCCAGGCCACGGATGTGTATGGGACCCTCGCCAAAGAC
CTAGTGCCAGAGGCCCAGGAATCAGTCTCCAGTGGGAGCAGCAGTGATGTCCAAGTCACAGATGCAAGTCTTGGTGAGGA
ATTCAAATAAGCCAAACTGAGT

Alignment

ORF - retro_cfam_2168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.61 %
• Parental protein coverage: 70.22 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRIMDPYKASYG-VEDPEYAVTQLAQTTMRSELGKLSLDKVFRERES-LNASIVDAINQAADCWGIRCLR
          L.I.D.YK.SY...EDPEYA.TQLAQ.T....L......K..R.R.....A.....I.QAADCWGI.CL.
Retrocopy LCILDSYKTSYN<LEDPEYAITQLAQRTINQSLENFLWKKSSRSRSL*MLAL*INTIIQAADCWGIHCLH

Parental  YEIKDIHVPPRVKESMQMQVEAERR-KRATVLESEGTRESAINVAEGKKQAQILASEAEKAEQINQAAGE
          YEI.DIHVP..VKESMQ..VEAE...K.ATVLESEG..ES..N...GK.QA.ILAS.AEK.EQIN.AAG.
Retrocopy YEINDIHVPL*VKESMQKEVEAEVE<KWATVLESEGIQESSNNLVKGKNQA*ILASQAEKPEQINKAAG*

Parental  ASAVLAKAKAKAEAIRILAAALTQHNGDAAASLTVAEQYVSAFSKLAKDSNTILLPSNPGDVTSMVAQAM
          ASAVLAK.KAKA....ILAA.LTQHNGDAAASLT.AEQY.S.FSKL...SNTILLPSNP..V..MVAQA.
Retrocopy ASAVLAKTKAKA---KILAAVLTQHNGDAAASLTMAEQYFSVFSKLV*YSNTILLPSNPCNVITMVAQAT

Parental  GVYGALTKAPVPGAQDSVSSGSSRDVQGTDASLDEEFDRVKLS
          .VYG.L.K..VP.AQ.SVSSGSS.DVQ.TDASL.EEF...KLS
Retrocopy DVYGTLAKDLVPEAQESVSSGSSSDVQVTDASLGEEFK*AKLS

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	63.96 RPM
SRP017611_brain	0.08 RPM	56.61 RPM
SRP017611_kidney	0.00 RPM	82.08 RPM
SRP017611_liver	0.00 RPM	33.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2168 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2168 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002000	1 retrocopy	retro_cfam_2168 ,