RetrogeneDB ID: retro_cjac_3256

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:118755084..118756056(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022252
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZYX
• Ensembl ID: ENSCJAG00000009741
• Aliases: None
• Description: None

Sequence

>retro_cjac_3256
GTGTCTTTGGCTAACACCCAGCCCTGAGGTCCCCCAGCCCCATCTCCGGCACCAGTCCCTAAGTTTTCTCCAGTGACTCC
TAAGTTTATTCCTGTGGCTTCCAAGTTTTGTCCTGGAGCCCCAGGTGGACCTGGGTCACAGCCGAATCAAAAATTGGGGC
ACCCGAAGCTATTTCCGCTGGCACAGGCACCCCTCAACCTCCCAGCTTCACCTATGCTCAGCAGAGGGAGAAGACCCGAG
TGCAGGAGAAGCAGCACCCTGTGCCCCCACAGGCTCAGAACCAAAACCAGGTGCGCTCCCCGGGGACCCCAGGGCCCCTG
ACTCTGAAAGAGGTGGAGGAGCTGGAGCAGCTGACTCAGCAGCTAATGCAGGACAGGAGCATCCTCACAGGCAGACGGTG
GCCGCCAATGAACTCTGCGGCCGATGCCATCAGCCCCTGGCCCGGGCTCAGCCGGCCGGCCGTGCCCTGGGGCAGCTGTT
CCACATCGCCTGCTTCACCTGCCACCAGTGCGCGCAGCAGCTCCAGGCCCAGCAGTTCTACAGCCTGGAGGGGGCGCTGT
GCGGCGAGGGCTGCAGCACTGACACCCTGGAGAAGTGCAACACCTGCGGGCAGCCCATCACCGACCGCGTGCTGAGGGCG
CGGGCAAAGCCTACCATCCGCAGTGCTTCACCTGTGTGGTCTGCGCCCGCCCCCTGGAGGGCACCTCCTTCATCGTGGAC
CAGGCCAACCGGCCCCACTGTGTCCCTGACCACCACAAGCAGTACGCCCCGAGGTGCTCCGTCAGCCCGGAGCCCATCAT
GCCTGAGCCTGGCCGAGATGAAACCGTGCGAGTGGTCGCCCTGGACAAGAACTTCCACATGAAGTGTTACAAGTGTGAGG
ACTGCGGGAAGCCCCTGTCCATTGAGGCAGATGACCATGGCTGCTTCCCCGGACGGTCACATGCTCTGTCGGAAGTGCCA
CACGGGTCGAGA

Alignment

ORF - retro_cjac_3256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.62 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSLANTQPRGSPAPSPAPAPKFSPVTPKFTPVASKFSPGAPGGPGSQPNQKLGHS-EAISAGTGTPQPPS
          VSLANTQP.G.PAPSPAP....................GAPGGPGSQPNQKLGH..EAISAGTGTPQPPS
Retrocopy VSLANTQP*GPPAPSPAPVXXXXXXXXXXXXXXXXXXXGAPGGPGSQPNQKLGHP<EAISAGTGTPQPPS

Parental  FTYAQQREKPRVQEKQHPVPPPAQNQNQVGSPGAPGPLTLKEVEELEQLTQQLMQD-MEHPQRQTVAANE
          FTYAQQREK.RVQEKQHPVPP.AQNQNQV.SPG.PGPLTLKEVEELEQLTQQLMQD..EHP.RQTVAANE
Retrocopy FTYAQQREKTRVQEKQHPVPPQAQNQNQVRSPGTPGPLTLKEVEELEQLTQQLMQD<QEHPHRQTVAANE

Parental  LCGQCHQPLARAQPAVRALGQLFHIACFTCHQCAQQLQGQQFYSLEGAPYCEGCYTDTLEKCNTCGQPIT
          LCG.CHQPLARAQPA.RALGQLFHIACFTCHQCAQQLQ.QQFYSLEGA...EGC.TDTLEKCNTCGQPIT
Retrocopy LCGRCHQPLARAQPAGRALGQLFHIACFTCHQCAQQLQAQQFYSLEGALCGEGCSTDTLEKCNTCGQPIT

Parental  DRMLRA-TGKAYHPQCFTCVVCARPLEGTSFIVDQANRPHCVSDYHKQYAPRCSVCSEPIMPEPGRDETV
          DR.LRA..GKAYHPQCFTCVVCARPLEGTSFIVDQANRPHCV.D.HKQYAPRCSV..EPIMPEPGRDETV
Retrocopy DRVLRA<AGKAYHPQCFTCVVCARPLEGTSFIVDQANRPHCVPDHHKQYAPRCSVSPEPIMPEPGRDETV

Parental  RVVALDKNFHMKCYKCEDCGKP-SIEADDNGCFPLDGHVLCRKCHTGR
          RVVALDKNFHMKCYKCEDCGKP.SIEADD.GCFP...H.L....H..R
Retrocopy RVVALDKNFHMKCYKCEDCGKPLSIEADDHGCFPGRSHALSEVPHGSR

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	0.00 RPM	6.01 RPM
SRP051959_heart	0.00 RPM	11.07 RPM
SRP051959_kidney	0.00 RPM	5.79 RPM
SRP051959_liver	0.00 RPM	5.76 RPM
SRP051959_lung	0.02 RPM	14.95 RPM
SRP051959_lymph_node	0.00 RPM	9.89 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.33 RPM
SRP051959_spleen	0.02 RPM	10.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3256 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3256 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	ENSCJAG00000009741	1 retrocopy	retro_cjac_3256 ,
Tursiops truncatus	ENSTTRG00000010808	1 retrocopy	retro_ttru_1565,