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 summary: | ||
| Parental gene symbol: | PCDHB2 | ||
| Ensembl ID: | ENSCJAG00000016152 | ||
| Aliases: | None | ||
| Description: | protocadherin beta 2 [Source:HGNC Symbol;Acc:8687] |
Retrocopy-Parental alignment summary:
>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
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1774 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1774 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1774 has 0 orthologous retrocopies within eutheria group .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 |