RetrogeneDB ID: retro_cjac_1024

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:32860389..32861746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PINK1
• Ensembl ID: ENSCJAG00000006493
• Aliases: None
• Description: None

Sequence

>retro_cjac_1024
CAGGCAAGTTTTACCGAGAAAAGCAAGCTAGGGTCTGATCCGTTGGACACCAGACGCTGGCAAGGCTTTCGGCTGGAGGA
GTAACTGATAGGGCAGTCCATTGGCAAGGGCTGCAGTGCCGCTGTGCATGAAGCCACCACGCCTACACTGCCCCAGAACC
TGGAGGTGACCAAGAGCACCAGGCTGCTTCCAGGGAGAGGCCCAGGTACCAGTGCACCTGGAGAAGAGCAGGAGCGAGCT
CCGGGGGCCCCTGCCTTCCCCTTGGCCATCAAGATGATGTGGAACATCTCGGCAGGTTCCTCCAGTGTAGCCATCTTGAA
CACAATGAGCCAGGAGCTGGTCCCAGCGAGCCTAGTGGCCTTGGCCGGGGTGTATGGAGCAGTTGCTTACAGAAAATCCA
AGAGAGGTCCCAAGCAACTAGCCCTTCACCCTAGTATCACCAGGGTTCTCCCCGCCTTCACCTCTTCTGTGCTGCTGCTG
CCAGGGGCCCTGGTCGACTACCCTGATGTGCTGCCCCACATCTCCACCCTGAAGGCCTGAGCCATGGCTGGACGCTGTTC
CTCGTCATGAAGAACTATCCCTGTACCCTGCTCCAGTACCTTCGCATGAACACACCCAGCCCCTGCCTGGCCACCATGAT
GGTGCTGCAGCTGCTAGAAGGCGTGGACCATCTGGTTCAACAGGGCATTGCACACAGAGACTTGAAATCTGACAACATCC
TCGTGGAGCTGGACCCAGATGGCTGCCCCTGGCTGGTGATCACAGATTTTGGCTGCTGCCTGGTTGATGAGAACATCGGC
CTGCATTTGCCCTTCAGCAGCTGGTGTGTGGATCGGGGCTGAAACGGCTGCCTGATGGCCCTGGAGGTGTCCACAGCCCA
TCCTGGCCCAGGGCAGTGATTGACTACCGCAAGGCTGATGCCTGGGCAGTGGGAGCCATTGCCTATGAAATCTTCGGGCT
TGTCGATCCCTTCTAGAGCCAGGATAAGGCCCACCTTGAAAGCCACAGTTATCAAGAGGCTCAACTACCTGCACTGCTCG
AGCTGGTGCCTCCAGACGCTAGACAACTGGTGAGGACACTGCTCCAGCGAGAGGCCAGCAAGAGACCATCTGCCTGAGTA
GCCGCTAATGTGCTTCATCTAAGCCTCTGGGGTGAACATATTCTACCCCTGAAGAATCGGAAGTTAGACAAGATGGTTGG
CTGGCTCCTCTAACAGTTGGCTGCCACTTTGTTGGCCAACAGGCTCACAGCGAAGTGTTGCGTGGAAACAAAAATGAAGA
TGCTCTTTCTGGCTAACCTGGAGTGTGAAGCACTCTGCCAGGCAGCCCTCCTCCTCTACTCATGGAGGGCAGCCCTG

Alignment

ORF - retro_cjac_1024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAIFTQKSKLGPDPLDTRRWQGFRLEEYLIGQSIGKGCSAAVYEATTPTLPQNLEVTKSTRMLPGRGPGT
          QA.FT.KSKLG.DPLDTRRWQGFRLEE.LIGQSIGKGCSAAV.EATTPTLPQNLEVTKSTR.LPGRGPGT
Retrocopy QASFTEKSKLGSDPLDTRRWQGFRLEE*LIGQSIGKGCSAAVHEATTPTLPQNLEVTKSTRLLPGRGPGT

Parental  SAPGEEQERAPGAPAFPLAIKMMWNISAGSSNEAILNTMSQELVPASRVALAGEYGAVAYRKSKRDPKQL
          SAPGEEQERAPGAPAFPLAIKMMWNISAGSS..AILNTMSQELVPAS.VALAG.YGAVAYRKSKR.PKQL
Retrocopy SAPGEEQERAPGAPAFPLAIKMMWNISAGSSSVAILNTMSQELVPASLVALAGVYGAVAYRKSKRGPKQL

Parental  APHPNIIRVLRAFTSSVPLLPGALVDYPDVLP-PRLHPEGLGHGRTLFLVMKNYPCTLRQYLRMNTPSPR
          A.HP.I.RVL.AFTSSV.LLPGALVDYPDVLP.P.LHPEGL.HG.TLFLVMKNYPCTL.QYLRMNTPSP.
Retrocopy ALHPSITRVLPAFTSSVLLLPGALVDYPDVLP<PHLHPEGLSHGWTLFLVMKNYPCTLLQYLRMNTPSPC

Parental  LATMMMLQLLEGVDHLVQQGIAHRDLKSDNILVELDPDGCPWLVITDFGCCLADENIGLHLPFSSWYVDR
          LATMM.LQLLEGVDHLVQQGIAHRDLKSDNILVELDPDGCPWLVITDFGCCL.DENIGLHLPFSSW.VDR
Retrocopy LATMMVLQLLEGVDHLVQQGIAHRDLKSDNILVELDPDGCPWLVITDFGCCLVDENIGLHLPFSSWCVDR

Parental  GGNGCLMAPEVSTARPG-PRAVIDYSKADAWAVGAIAYEIFGLVNPFYGQGKAHLESRSYQEAQLPALPE
          G.NGCLMA.EVSTA.PG.PRAVIDY.KADAWAVGAIAYEIFGLV.PF..Q.KAHLES.SYQEAQLPAL.E
Retrocopy G*NGCLMALEVSTAHPG<PRAVIDYRKADAWAVGAIAYEIFGLVDPF*SQDKAHLESHSYQEAQLPALLE

Parental  LVPPDARQLVRALLQREASKRPSARVAANVLHLSLWGEHILPLKNLKLDKMVGWLLQQSAATLLANRLTA
          LVPPDARQLVR.LLQREASKRPSA.VAANVLHLSLWGEHILPLKN.KLDKMVGWLL.Q.AATLLANRLTA
Retrocopy LVPPDARQLVRTLLQREASKRPSA*VAANVLHLSLWGEHILPLKNRKLDKMVGWLL*QLAATLLANRLTA

Parental  KCCVETKMKMLFLANLECEALCQAALLLCSWRAAL
          KCCVETKMKMLFLANLECEALCQAALLL.SWRAAL
Retrocopy KCCVETKMKMLFLANLECEALCQAALLLYSWRAAL

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	0.13 RPM	16.37 RPM
SRP051959_heart	0.12 RPM	50.11 RPM
SRP051959_kidney	0.09 RPM	40.84 RPM
SRP051959_liver	0.22 RPM	50.73 RPM
SRP051959_lung	0.29 RPM	13.27 RPM
SRP051959_lymph_node	0.23 RPM	8.58 RPM
SRP051959_skeletal_muscle	0.07 RPM	52.83 RPM
SRP051959_spleen	0.27 RPM	10.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1024 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006493	1 retrocopy	retro_cjac_1024 ,
Macaca mulatta	ENSMMUG00000008835	1 retrocopy	retro_mmul_225,
Nomascus leucogenys	ENSNLEG00000007921	1 retrocopy	retro_nleu_3022,