RetrogeneDB ID: retro_cjac_1774

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:38175513..38177871(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034178
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCDHB2
• Ensembl ID: ENSCJAG00000016152
• Aliases: None
• Description: protocadherin beta 2 [Source:HGNC Symbol;Acc:8687]

Sequence

>retro_cjac_1774
CAAAAAAGGCAAGTTCTGATATTCTTTGTTTTGCTGGGATTGTCTCAGGCAGGTACTGAATCTGCACACTATTCTGTTGC
AGAGGAAACAGAAATTGGCTCTTTTGTGGCCAATCTGGCGAGGGACCTAGGGCTGGAGGTGGAGGAGCTGTCTTCACGGG
AAGCCCGGGTAATGTCTGATTATAATAAAAAGTATTTGCACCTTGATTTGCTGACTGGGGACTTGCTCCTAAATGAGAAA
CTAGACCGAGAAGAGCTGTGTGGCTCCACCGAGCCCTGTGTGCTACATTTTCAGGTGGTTTTGGAAAACCCTTTGCAGTT
TTTTCAGGTTGAGCTGCATGTCAAAGACATAAATGATCACTCCCCTACATTCCTAGACAATGAAATACTTATTAAAATAT
CAGAAGGTACCACTGTTGGAACTACATTCCTATTGGAGAGTGCTCGAGATTTGGATGTCGGAAGCAACAGTCTCCAAAAC
TACACAATTAGCCCCAATTCTCACTTCTATATTAAAATTCCAGACAGTGGTGACAGAAAGATATACCCAGAGCTGGTCCT
AGATAGAGCTTTAGATTATGAGGAGGAAGCTGAACTCAGATTAACACTCACGGCACTGGACGGCGGATCCCCACCCAGGT
CTGGGACAACTTTGGTTCTCATTAAGGTGTTGGACATCAATGATAATGCCCCTGAGTTTCCTCAGAGTCTCTATGAGGTG
CAGGTCCCTGAGGATAGACCCCTTGGCTCCTGGATTGTTACCATCTCAGCTAAGGATTTGGATACAGGAAACTATGGGAA
AATATCTTACACATTTTCCCATGCATCAGAAGATATTCGTAAAACATTTGAAATCAATCCAATGTCTGGAGAAGTTAATT
TGAGATCACCCCTGGATTTTGAAGCAATACAGTCCTATACTATAAATATTCAGGCAACAGATGGTGGGGGTCTTTCAGAA
AAATGCACTCTTCTAGTTAAAGTTACGGATATAAACGACAACCCACCAAAAGTGACCATGTCGTCGATTACAAAAAGAAT
TCCAGAGAATGCCTCAGAGACCCTAGTAGCTCTTTTTAGTGTCCTAGACCAAGATTCTGAGGACAATGGGAGGATGATTT
GCTCTATTCAGGATAATCTCCCTTTTATCCTGAAACCGACCTTCAAGAACTTTTTCACAATAGTTTCTGAAAAAGCACTG
GACAGAGAGAGCCAAGCCGAGTACAACATCACCATCACCGTCACTGACTTGGGAACGCCTAGGCTGAAAACCGAGTACAA
CATAACCGTGCTGGTGTCCGACGTCAACGACAACGCCCCTGCTTTCACCCAAACTTCCTACATCCTCTTCGTCCGCGAGA
ACAACAGCCCCGCCCTGCACATTGGCACCGTCAGCGCCACAGACAGAGACTCAGGCACCAACGCACAGGTCACCTACTCG
CTGCTGCCGCCCCAGGACACGCACCTGCCCCTCGCCTCCCTGGTCTCCATCAACCCGGACAACGGACACCTGTTCGCCCT
CCGGTCCCTGGACTACGAGGCCCTGCAGGCGTTCGAGTTCCGCGTGGGCGCCACAGACCGCGGCTCTCCGGCGCTGAGCA
GCGAGGCGCTGGTGCGCGTGCTGGTGCTGGACGCCAACGACAACTCGCCCTTCGTGCTGTACCCGCTGCAGAACGGCTCC
GCGCCCTGCACCGAGCTGGTGCCCCGGGTGGCCGAGCCGGGCTACCTGGTGACCAAGGTGGTGGCGGTGGACGGCGACTC
GGGCCAGAACGCCTGGCTGTCGTTCCAGCTGCTCAAGGCCACTGAGCCCGGGCTGTTCGGCGTGTGGGCGCACAATGGCG
AGGTGCGCACCGCCAGGCTGCTGAGCGAGCGCGACGCGGCCAAGCACAGGCTGCTGGTGCTGGTCAAGGACAATGGCGAG
CCTCCGCGCTCGGCCACCGCCACGCTGCACGTGCTCCTGGTGGACGGCTTCTCCCAGCCCTACCTGCCGCTCCCGGAGGC
GGCCCCGGCCCAGGCCCAGGCCGACTCGCTCACCGTCTACCTGGTGGTGGCGTTGGCCTCGGTGTCGTCGCTCTTCCTGT
TCTCGGTGCTCCTGTTCGTGGCGGTGCGGCTGTGCAGGAGGAGCAGGGCGGCCTCTGTGGGTCGCTGCTCGGTGCCCGAG
GGCCCCTTTCCAGAGCCTCTGATGGACGTGAGCGGCACCGGGACCCTGTCCCAGAGCTACCAGTACGAGGTGTGTCTGAT
GGGAGGTTCCGGGACAAATGAGTTCAAATTTCTGAAGCCAATTATCCCCAGTTTTCAAGTTCATGACGCTGGTAAGAATA
TGGGGGAAATCAAGAACTATCGGAATAGCTTTGGATTT

Alignment

ORF - retro_cjac_1774 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQRQVVIFFVLLGIAQASSQPRHYSVAEETESGSFVANLLKDLGLEVRELAVRGARVVSKGKKMHLQFDR
          ..RQV.IFFVLLG..QA.....HYSVAEETE.GSFVANL..DLGLEV.EL..R.ARV.S...K..L..D.
Retrocopy QKRQVLIFFVLLGLSQAGTESAHYSVAEETEIGSFVANLARDLGLEVEELSSREARVMSDYNKKYLHLDL

Parental  QTGDLLLNEKLDREELCGPTEPCVLPFQVLLENPLQFFQAELRIRDINDHPPVFLDKEILLKISESITPG
          .TGDLLLNEKLDREELCG.TEPCVL.FQV.LENPLQFFQ.EL...DINDH.P.FLD.EIL.KISE..T.G
Retrocopy LTGDLLLNEKLDREELCGSTEPCVLHFQVVLENPLQFFQVELHVKDINDHSPTFLDNEILIKISEGTTVG

Parental  TTFLLERAQDLDVGTNSLQNYTISPNFHFHLNLQDNPDGTILPQLVLDRALDREEQPEIRLTLTALDGGT
          TTFLLE.A.DLDVG.NSLQNYTISPN.HF.....D..D..I.P.LVLDRALD.EE..E.RLTLTALDGG.
Retrocopy TTFLLESARDLDVGSNSLQNYTISPNSHFYIKIPDSGDRKIYPELVLDRALDYEEEAELRLTLTALDGGS

Parental  PPKSGTALVRIEVVDINDNIPEFAKLLYEVQVPEDSPVGSQVATVSARDLDIGTNGEISYAFSQASEDIR
          PP.SGT.LV.I.V.DINDN.PEF...LYEVQVPED.P.GS...T.SA.DLD.G..G.ISY.FS.ASEDIR
Retrocopy PPRSGTTLVLIKVLDINDNAPEFPQSLYEVQVPEDRPLGSWIVTISAKDLDTGNYGKISYTFSHASEDIR

Parental  KTFRLSAKSGELLLRQKLDFESIQTYTVNIQATDGGGLSGKSTVVVQVVDVNDNPPELTLSSVNSPVPEN
          KTF.....SGE..LR..LDFE.IQ.YT.NIQATDGGGLS.K.T..V.V.D.NDNPP..T.SS.....PEN
Retrocopy KTFEINPMSGEVNLRSPLDFEAIQSYTINIQATDGGGLSEKCTLLVKVTDINDNPPKVTMSSITKRIPEN

Parental  SAETVLAVFRIRDRDSGDNGKMICSIPDNLPFILKPTLKNFYTLVTERPLDRETRAEYNIIIIVTDLGTP
          ..ET..A.F...D.DS.DNG.MICSI.DNLPFILKPT.KNF.T.V.E..LDRE..AEYNI.I.VTDLGTP
Retrocopy ASETLVALFSVLDQDSEDNGRMICSIQDNLPFILKPTFKNFFTIVSEKALDRESQAEYNITITVTDLGTP

Parental  RLKTEHSITVRVSDVNDNAPAFTQTSYTLFVRENNSPALHIGTVSATDRDSGTNAQVTYSLLQPQDPHLP
          RLKTE..ITV.VSDVNDNAPAFTQTSY.LFVRENNSPALHIGTVSATDRDSGTNAQVTYSLL.PQD.HLP
Retrocopy RLKTEYNITVLVSDVNDNAPAFTQTSYILFVRENNSPALHIGTVSATDRDSGTNAQVTYSLLPPQDTHLP

Parental  LASLVSINADNGHLFALRSLDYEALQAFEFRVGATDRGSPALSSEALVRVLVLDANDNSPFVLYPLQNGS
          LASLVSIN.DNGHLFALRSLDYEALQAFEFRVGATDRGSPALSSEALVRVLVLDANDNSPFVLYPLQNGS
Retrocopy LASLVSINPDNGHLFALRSLDYEALQAFEFRVGATDRGSPALSSEALVRVLVLDANDNSPFVLYPLQNGS

Parental  APCTELVPRVAEPGYLVTKVVAVDGDSGQNAWLSFQLLKATEPGLFGVWAHNGEVRTARLLSERDAAKHR
          APCTELVPRVAEPGYLVTKVVAVDGDSGQNAWLSFQLLKATEPGLFGVWAHNGEVRTARLLSERDAAKHR
Retrocopy APCTELVPRVAEPGYLVTKVVAVDGDSGQNAWLSFQLLKATEPGLFGVWAHNGEVRTARLLSERDAAKHR

Parental  LLVLVKDNGEPPRSATATLHVLLVDGFSQPYLPLPEAAPAQAQADSLTVYLVVALASVSSLFLFSVLLFV
          LLVLVKDNGEPPRSATATLHVLLVDGFSQPYLPLPEAAPAQAQADSLTVYLVVALASVSSLFLFSVLLFV
Retrocopy LLVLVKDNGEPPRSATATLHVLLVDGFSQPYLPLPEAAPAQAQADSLTVYLVVALASVSSLFLFSVLLFV

Parental  AVRLCRRSRAASVGGCSVTEGPFPGHLVDVSGTGTLSQSYQYEVCLTGGSATNEFKFLKPIIPNFLPQNT
          AVRLCRRSRAASVG.CSV.EGPFP..L.DVSGTGTLSQSYQYEVCL.GGS.TNEFKFLKPIIP.F.....
Retrocopy AVRLCRRSRAASVGRCSVPEGPFPEPLMDVSGTGTLSQSYQYEVCLMGGSGTNEFKFLKPIIPSFQVHDA

Parental  GREVEENPPFQNNLGF
          G....E.....N..GF
Retrocopy GKNMGEIKNYRNSFGF

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
SRP051959_colon	2.46 RPM	1.95 RPM
SRP051959_heart	4.67 RPM	3.14 RPM
SRP051959_kidney	0.75 RPM	1.31 RPM
SRP051959_liver	1.43 RPM	0.37 RPM
SRP051959_lung	0.89 RPM	1.63 RPM
SRP051959_lymph_node	0.21 RPM	0.68 RPM
SRP051959_skeletal_muscle	0.33 RPM	1.18 RPM
SRP051959_spleen	0.88 RPM	1.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1774 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1774 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016152	1 retrocopy	retro_cjac_1774 ,
Oryctolagus cuniculus	ENSOCUG00000010930	1 retrocopy	retro_ocun_1159,