RetrogeneDB ID: retro_cjac_4018

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288546.1:10500..11290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUS1L
• Ensembl ID: ENSCJAG00000018104
• Aliases: None
• Description: None

Sequence

>retro_cjac_4018
ATGCCAAAGCTGCAGGGCTTCGAGTTCTGGAGTCACACCCTTCGGGGTCCCGCCACTTGGTGGTCCCCATGGTGGACCAG
AGCGAGCTGGCCTGGAGGCTGCTGAGCTGGCGCCAAGGGGCACAGCTCTGCTACACGCCCATGCTGCACGCCCAAGTCTT
CGTCTGTGACGCCAATTACCAGAAGGAGAACCTGTACTGTGAGGTGTGCCCCGAGGGCCGGCCCCTCATGGTGCAGTTCT
GTGCCAATGATCCGGAGGTGTTTGTTCAGGCGGCTCTCCTGGCTCTGGGTTACTGTGACGCCATCGACCTGAACCTGGGC
TGTCCACAGATGATAGCCAAGAGAGGTCACTATGGCGCCTTCCTGCATGTTGAGTGGAACCTGCTCCAAAGAATAATTTT
GCTGGCCCACAAGAAACTCTCTGTTCCCTTCATGTGCAAAATCTGTGTCTTCCCAGAGATTGACAAGACCGTGAGATAGG
CCCAGATGCTGGAGAAGGCTGGCTGCCAGTTGCTGACCGTCCATGGGTACGCCAAGGAGCAGAAGGGGCCCGGTCGGGTG
CAGCGTCCTGGGAGCACATTAAGGCTTTGCAGAAAGCTGTGGCCATCGCTGTGTTTGCCAATGGGCACATCCAGAGCCTA
CAGGATGTGGAGCGCTGCATCCAGGACACGGGTGTACAGGGTGTCATGAGCGCAGAAGGTAACCTGCACAACTCTGTCCT
GTTTGAGGGCTGGAGCCCTGCCGTTTGGAAGCTGGCCGATGAATACCTGGACATCGTGTGGGAGCACCCC

Alignment

ORF - retro_cjac_4018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKLQGFEFWSHTLRG-ARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEV
          MPKLQGFEFWSHTLRG..RH.V.PMVDQSELAWRLLS.R.GAQLCYTPMLHAQVFV.DANY.KENLYCEV
Retrocopy MPKLQGFEFWSHTLRG<SRHLVVPMVDQSELAWRLLSWRQGAQLCYTPMLHAQVFVCDANYQKENLYCEV

Parental  CPEDRPLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEK
          CPE.RPL.VQFCANDPEVFVQ.ALL..GYCDAID.N.GCPQMIAKRGHYGAFL..EW.LLQR.ILLAH.K
Retrocopy CPEGRPLMVQFCANDPEVFVQAALLALGYCDAIDLNLGCPQMIAKRGHYGAFLHVEWNLLQRIILLAHKK

Parental  LSVPVTCKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVP-LSSAASWEHIKAVRKAVAIPVFAN
          LSVP..CKI.VFPEIDKTVR.AQMLEKAGCQLL.VHG..K.QK.P..S.AASWEHIKA..KAVAI.VFAN
Retrocopy LSVPFMCKICVFPEIDKTVR*AQMLEKAGCQLLTVHGYAKEQKGP<RSGAASWEHIKALQKAVAIAVFAN

Parental  GNIQSLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHP
          G.IQSLQDVERCIQDTGVQGVMSAEGNLHN..LFEG.SPAVW.LA.EYLDIV.EHP
Retrocopy GHIQSLQDVERCIQDTGVQGVMSAEGNLHNSVLFEGWSPAVWKLADEYLDIVWEHP

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	12.31 RPM
SRP051959_heart	0.00 RPM	10.26 RPM
SRP051959_kidney	0.00 RPM	15.29 RPM
SRP051959_liver	0.00 RPM	24.11 RPM
SRP051959_lung	0.00 RPM	11.26 RPM
SRP051959_lymph_node	0.00 RPM	12.15 RPM
SRP051959_skeletal_muscle	0.04 RPM	30.97 RPM
SRP051959_spleen	0.00 RPM	12.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4018 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4018 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018104	5 retrocopies	retro_cjac_1422, retro_cjac_1887, retro_cjac_3451, retro_cjac_4002, retro_cjac_4018 ,
Monodelphis domestica	ENSMODG00000003351	1 retrocopy	retro_mdom_1097,
Pan troglodytes	ENSPTRG00000009790	1 retrocopy	retro_ptro_883,