RetrogeneDB ID: retro_cjac_2966

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:19422462..19423304(-)
• Located in intron of: ENSCJAG00000008044

Retrocopy information

• Ensembl ID: ENSCJAG00000008077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BPHL
• Ensembl ID: ENSCJAG00000017700
• Aliases: None
• Description: biphenyl hydrolase-like (serine hydrolase) [Source:HGNC Symbol;Acc:1094]

Sequence

>retro_cjac_2966
CTGCAGCTGCGGCTGCTGCTCTGGGCACTGACGCCCAGTATCCTCGTCCCACAGGCCTGACCCGCGGCAGCGTTCAGCAC
CTTGGTAACCTCTGCCAAAGTGGCTGTGAATGGCATCCATCTGTATTACCAGCAGGCTGGAGAGGGAGATCACGCAGTCC
TGCTACTTCCTGGGATGTTGGGAAGTGGAGAGACTGATTCCGGACCTCAGCTCACGAACCTCAATAAGAAGCTCTTTAAA
GTGGTCGCCTGGGATCCTGGAGGCTATGGGCATTCCAAGCCTTCACATCGCGATTTCCCAGTAGACTTTTTTGAAAGAGA
CGCAAAAGATGCTGTTGATTTGATGAAGGCGCTGAAGTTTAAGAAGGTTTCTCTGCCGGGGTGGAGTGATGGGGGCATAA
CCGCACTCACTGCTGCTGCAAAATACCCATCTTACATCCACAAGATGGTGATTTGGGGCCCCAATGCCTACGTCACTGAT
GAAGACAGCATGTCTTACGAGGGCATCGAGATTTTTCTAAATGGCGTGAGAGAACAAAAAAGCCTCTAGAAGCCCCCTAT
GGGCATGACTACTTTGCCAGAACCTGTGAAAAGTGGGTGGATGGCATAAGCCTGTTTAAACATCTTCCAGATGGTAACAT
CTGCCAGCACCTGCTGCCCCAGGTCCAGCGCCCCACCTTGATTGTGCATGGCGAGAAGTATCTTCTGGTCCTAAGGTTTC
ATGCCGACTTCATTCATTGGCACGTGAAAGGCTCACGGCTGCATTTGATGCCAGAAAGCAAACACAACCTGCATTTGCGT
TTTGCAGATGAATTTAACAAGTTAGCAGAAGACTTCCTACAA

Alignment

ORF - retro_cjac_2966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.82 %
• Parental protein coverage: 95.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRLRMLLTALKPGVLVSQAGPAAAFGTSITSAKVAVNGVHLHYQQTGEGDHAVLLLPGMLGSGETDFGPQ
          L.LR.LL.AL.P..LV.QA.PAAAF.T..TSAKVAVNG.HL.YQQ.GEGDHAVLLLPGMLGSGETD.GPQ
Retrocopy LQLRLLLWALTPSILVPQA*PAAAFSTLVTSAKVAVNGIHLYYQQAGEGDHAVLLLPGMLGSGETDSGPQ

Parental  LKNLNKKLFTVVALDPRGYGHSKPPDRDFPVDFFERDAKDAVDLMKALKFKKVSLLGWSDGGITALIAAA
          L.NLNKKLF.VVA.DP.GYGHSKP..RDFPVDFFERDAKDAVDLMKALKFKKVSL.GWSDGGITAL.AAA
Retrocopy LTNLNKKLFKVVAWDPGGYGHSKPSHRDFPVDFFERDAKDAVDLMKALKFKKVSLPGWSDGGITALTAAA

Parental  KYPSYIRKMVIWGANAYVTDEDSVIYEGI-RDVSKWSERTKKPLEALYGYDYFARTCEKWVDGISQFKHL
          KYPSYI.KMVIWG.NAYVTDEDS..YEGI.RD.SKW.ERTKKPLEA.YG.DYFARTCEKWVDGIS.FKHL
Retrocopy KYPSYIHKMVIWGPNAYVTDEDSMSYEGI<RDFSKWRERTKKPLEAPYGHDYFARTCEKWVDGISLFKHL

Parental  PDGNICRHLLPQVQCPTLIVHGEKDPLVPRFHADFIHEHVKGSRLHLMPEGKHNLHLRFADEFNKLAEDF
          PDGNIC.HLLPQVQ.PTLIVHGEK..LV.RFHADFIH.HVKGSRLHLMPE.KHNLHLRFADEFNKLAEDF
Retrocopy PDGNICQHLLPQVQRPTLIVHGEKYLLVLRFHADFIHWHVKGSRLHLMPESKHNLHLRFADEFNKLAEDF

Parental  LQ
          LQ
Retrocopy LQ

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	0.44 RPM	4.53 RPM
SRP051959_heart	0.56 RPM	5.77 RPM
SRP051959_kidney	0.58 RPM	7.52 RPM
SRP051959_liver	0.50 RPM	5.31 RPM
SRP051959_lung	0.57 RPM	4.91 RPM
SRP051959_lymph_node	0.37 RPM	5.07 RPM
SRP051959_skeletal_muscle	0.83 RPM	2.58 RPM
SRP051959_spleen	0.40 RPM	3.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2966 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2966 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
Callithrix jacchus	ENSCJAG00000017700	1 retrocopy	retro_cjac_2966 ,