RetrogeneDB ID: retro_cjac_3451

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180158.1:1064..2474(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3451
ATGCCAAAGCTGCAGGGCTTCGAGTTCTGGAGTCACAGCCTTCGGGGGGCCCGCCACGTGGTGGCCCCCATGGTGGACCA
GAGCGAGCTGGGCTGGAGGCTGCTGAGCCGGCGCCACGGGGCACAGCTCTGCTGCACGCCCACGCTGCATGCCCAAGTCT
TCGTCTGCGACGCCAATTACCGGAAGGAGAACCTGTACTGTGAGGCGTGCCCCGAGGACCGGCCCCTCATCATGCAGTTC
TGTGCCAATGACCCGGAGGTGTTTGTTCAGGCGGCTCTCCTGGCTCAGGATTACTGTGACGCCATCGACCTGAACCTGGG
CTGCCCACAGACAATAGCCAAGAGAGGTCACTATGGCGCCTTCCTGCAGGACGAGTGGAACCTGCTCCAAAGAATAATTT
TGCTGGCCCACGAGAAACTCTCTGTTCCCGTCACGTGCAGAATCCGTGTCTTCCCAGAGATTGACAAGACCGTGAGGTAT
GCCCAGATGCTGGAGAAGGCCGGCTGCCAGTTGCTGACTGTTCATGGGCGCACCAAGGAGCAGAAGGGGCCCCTGGCAGG
TGCAGCGTCCTGGGAGCGCATTAAGGCTGTGCGGAAAGCTGTGGCCATCCCTGTGTTTGCCGATGGGAACATTCAGAGCC
TGCAGGATGTGGAGCGCTGCATCCAGGACACGGGTGTGCAGGGTGTCATGAGCGCAGAAGGCAACCTGCATAACCCTGCC
CTGTTTGAGGGCCGGAGCCCTGCCGTGTGGGAGCTGGCCGAGGAATACCTGGACATCGTGCGGGAGCACCTCTGCCCACT
GTCCTACGTCTGGGCCCACCTCTTCAAGCTGTGGCACCACACGCTGCAGGTGCATCAGCAGCTGCGAGAGGAGCTGGCTA
AGGTGAAGACCCTGGAGGGCATTGCCGCCATGAGCCAGGAGCTGAAGATGCGGTGTCAAGAGGAGATGTCCAGGCCGGAG
GGAGCGAAGCCCGCCGGCGACTTGCCCTTCCACTGGATCTGCCAGCCCTACGTCCGGCCGGGGCCCAGGGAGGGGAGCAA
GGAGAAGGCAGGTGGGCGCAGCAAGCGGGCCCTGGAGGAGTGTGGCACGAAAGTCCTGTCCAAGAACAAGCAGAAGCAGC
AGCTGAGGAACCCCCACAAGACCTTTGACCCCTCTCTGAAGCCAAAATACGCAAAGTGTGACCGGTGTGGTAACCCAAAG
GGCAACAGATGTGTGTTCAGCCTGTGCCACGGCTGCTGCAAGAGGCGAGCCTCCAAAGAGACCGCGGACTGCCCAGGTCA
CGGATTGCTTTTTAAAACCAAATTGGAGAAGTCTTTGGCCTGGAAAGGGACCCAGCCTGAGCTGCAGGAGCCTCAGACAG
CCACGCCCCGCACACCAGGTGGCTTCTCAGAAGTCATGAGTAGTGCTCTG

Alignment

ORF - retro_cjac_3451 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKLQGFEFWSHTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC
          MPKLQGFEFWSH.LRGARHVVAPMVDQSEL.WRLLSRRHGAQLC.TP.LHAQVFV.DANYRKENLYCE.C
Retrocopy MPKLQGFEFWSHSLRGARHVVAPMVDQSELGWRLLSRRHGAQLCCTPTLHAQVFVCDANYRKENLYCEAC

Parental  PEDRPLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
          PEDRPLI.QFCANDPEVFVQ.ALL.Q.YCDAID.N.GCPQ.IAKRGHYGAFLQDEW.LLQR.ILLAHEKL
Retrocopy PEDRPLIMQFCANDPEVFVQAALLAQDYCDAIDLNLGCPQTIAKRGHYGAFLQDEWNLLQRIILLAHEKL

Parental  SVPVTCKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEHIKAVRKAVAIPVFANGN
          SVPVTC.I.VFPEIDKTVRYAQMLEKAGCQLL.VHG.TK.QK.PL..AASWE.IKAVRKAVAIPVFA.GN
Retrocopy SVPVTCRIRVFPEIDKTVRYAQMLEKAGCQLLTVHGRTKEQKGPLAGAASWERIKAVRKAVAIPVFADGN

Parental  IQSLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHH
          IQSLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREH.CPLSYV.AHLFKLWHH
Retrocopy IQSLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHLCPLSYVWAHLFKLWHH

Parental  TLQVHQQLREELAKVKTLEGIAAVSQELKMRCQEEISRQEGAKPTGNLPFHWICQPYVRPGPRERSKEKA
          TLQVHQQLREELAKVKTLEGIAA.SQELKMRCQEE.SR.EGAKP.G.LPFHWICQPYVRPGPRE.SKEKA
Retrocopy TLQVHQQLREELAKVKTLEGIAAMSQELKMRCQEEMSRPEGAKPAGDLPFHWICQPYVRPGPREGSKEKA

Parental  GARSKRALEEEEECGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKRRA
          G.RSKRALEE...CGT.VLSKNKQK.QLRNPHKTFDPSLKPKYAKCD.CGNPKGNRCVFSLC.GCCKRRA
Retrocopy GGRSKRALEE---CGTKVLSKNKQKQQLRNPHKTFDPSLKPKYAKCDRCGNPKGNRCVFSLCHGCCKRRA

Parental  SKETADCPGHGLLFKTKLEKSLIWKGTQPELQEPQTATPGTPGGFSEVMSSAL
          SKETADCPGHGLLFKTKLEKSL.WKGTQPELQEPQTATP.TPGGFSEVMSSAL
Retrocopy SKETADCPGHGLLFKTKLEKSLAWKGTQPELQEPQTATPRTPGGFSEVMSSAL

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	0.71 RPM	12.31 RPM
SRP051959_heart	0.39 RPM	10.26 RPM
SRP051959_kidney	0.47 RPM	15.29 RPM
SRP051959_liver	1.30 RPM	24.11 RPM
SRP051959_lung	0.49 RPM	11.26 RPM
SRP051959_lymph_node	0.48 RPM	12.15 RPM
SRP051959_skeletal_muscle	1.83 RPM	30.97 RPM
SRP051959_spleen	0.63 RPM	12.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3451 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3451 has 0 orthologous retrocopies within eutheria group .

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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,