RetrogeneDB ID: retro_cjac_4002

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL287515.1:7229..8601(+)
• 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_4002
GGGGCCCGCCACGTCGTGGCCCCCATGGTAGACCAGAGCGAGCTGGCCTGGAGGCTGCTGAGTCAGCGCCACAGGGCACA
GCTCTGCTACACGCCCATGCTGCACACCCAAGTCTTCGTCTGCCATGCTAATTACTGGAAGGAGAACCTGTACTGTGAGT
TGTGCCCCAAGGACCGGTCCCTCATGGTGCAGTTCTGTGCCAATGACCTGTAGGTGTTTGTTCAGGCAGCTCTCATGGCT
CAGAATTACTGTGATGCCATCGACCTGAACCTGGGCTGCCCACAGATGATAGCCAAGAGAGGTCACTATGACGCCTTCCT
GCAGGACGAGTGGAACCTGCTCCAAAAAATAATTTTGCTGGCCCACAAGAAACTCTCTGTTCCCGTCATGTGCAAAATCT
GTGTCTTCCCAGAGATTGACAAGACTGTGAGGTATGCCCAGATGCTGGAGAAGGCCGACTGCCAGTTGCTGACCGTTCAT
AAGTGCAAAGGAGCAGAAGGGGCCCCGGTCGGGTGCAGTGTCCTGAAAGAACATTAAGGCTGTGCAGAAAGCTGTGGCCA
TCCCTGTTTTCACCAATGGGAACATCCAGAGCCTACAGGATGTGGAGCGCTGCATCCAGGACACGGGTGTACAGGGTGTC
ATGAGCGCAGAAGGCAACCTGCACAACCCTGCCCTGTTTGAGGGCCAGAGCCCTGCCGTGTAGAAACTGGCCAGTGAATA
CCTGGACATCATGTGGGAGCTCCCCTGTCCACTGTCCTACGTCCGGGCCTACCTCTTCAAGCTGTGGCACCACATGCTGA
AGGTGCATCAGCAGCTGTGAGAGGAGCTGGCCAAGGCAAAATCCCTGGAGGGCATTGCTGCTGTGAGCCAGAAGCTGAAG
ATGCGGTGTCAGGAGGAGATATCCAGGCAGGAGGGAGTGAAGCCCACCAGCGACTTGCCCTTCCTCTGGATCTGCCAGCC
CTATGTCCGGCCGGGGCCCAGGGAGGGGAGCAAGGAGAAGGCAGGTGGGTGCAGCAAGTGGGCCCTGGAGGAGGAGGAGT
GTGGCATGAAAGTCCTGTCCAAGAACAAGCAGAAGAGGCAGCTGAAGAACCCCCACAAGACCTCTGACCCCTCTCTGAAG
TTAAAATATGCAATATGTGACCAGTGTGGCAACCCAAAGGGCAACAGATGTGTGTTCAGCCTGTGCCACGGCTGCTGCAA
GAGGTGAGCTGCCAAAGAGACCACGGACTGCCCAGGTCATGGATTGCTTTTTAAAACCAAATTGGAGAAGTTTTTGGCCT
GGAAAGGGACCCAGCCTGAGCTGCAGCCGCCTCTGACTGCCACGCCCCGCACACCAGGTGACTTCTCAGAAGTCATGAGT
AGTGCTCTGGCC

Alignment

ORF - retro_cjac_4002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.91 %
• Parental protein coverage: 96.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCANDP
          GARHVVAPMVDQSELAWRLLS.RH.AQLCYTPMLH.QVFV..ANY.KENLYCE.CP.DR.L.VQFCAND.
Retrocopy GARHVVAPMVDQSELAWRLLSQRHRAQLCYTPMLHTQVFVCHANYWKENLYCELCPKDRSLMVQFCANDL

Parental  EVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLSVPVTCKILVFPEID
          .VFVQ.AL..Q.YCDAID.N.GCPQMIAKRGHY.AFLQDEW.LLQ..ILLAH.KLSVPV.CKI.VFPEID
Retrocopy *VFVQAALMAQNYCDAIDLNLGCPQMIAKRGHYDAFLQDEWNLLQKIILLAHKKLSVPVMCKICVFPEID

Parental  KTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEH-IKAVRK-AVAIPVFANGNIQSLQDVERCIQD
          KTVRYAQMLEKA.CQLL.VH.C......P.......EH.....RK.AVAIPVF.NGNIQSLQDVERCIQD
Retrocopy KTVRYAQMLEKADCQLLTVHKCKGAEGAPVGCSVLKEH<LRLCRK<AVAIPVFTNGNIQSLQDVERCIQD

Parental  TGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHHTLQVHQQLREELA
          TGVQGVMSAEGNLHNPALFEG.SPAV..LA.EYLDI..E.PCPLSYVRA.LFKLWHH.L.VHQQL.EELA
Retrocopy TGVQGVMSAEGNLHNPALFEGQSPAV*KLASEYLDIMWELPCPLSYVRAYLFKLWHHMLKVHQQL*EELA

Parental  KVKTLEGIAAVSQELKMRCQEEISRQEGAKPTGNLPFHWICQPYVRPGPRERSKEKAGARSKRALEEEEE
          K.K.LEGIAAVSQ.LKMRCQEEISRQEG.KPT..LPF.WICQPYVRPGPRE.SKEKAG..SK.AL.EEEE
Retrocopy KAKSLEGIAAVSQKLKMRCQEEISRQEGVKPTSDLPFLWICQPYVRPGPREGSKEKAGGCSKWAL-EEEE

Parental  CGTEVLSKNKQKKQLRNPHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKRRASKETADCPGHGLL
          CG..VLSKNKQK.QL.NPHKT.DPSLK.KYA.CDQCGNPKGNRCVFSLC.GCCKR.A.KET.DCPGHGLL
Retrocopy CGMKVLSKNKQKRQLKNPHKTSDPSLKLKYAICDQCGNPKGNRCVFSLCHGCCKR*AAKETTDCPGHGLL

Parental  FKTKLEKSLIWKGTQPELQEPQTATPGTPGGFSEVMSSALA
          FKTKLEK.L.WKGTQPELQ.P.TATP.TPG.FSEVMSSALA
Retrocopy FKTKLEKFLAWKGTQPELQPPLTATPRTPGDFSEVMSSALA

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	0.02 RPM	12.31 RPM
SRP051959_heart	0.02 RPM	10.26 RPM
SRP051959_kidney	0.00 RPM	15.29 RPM
SRP051959_liver	0.04 RPM	24.11 RPM
SRP051959_lung	0.03 RPM	11.26 RPM
SRP051959_lymph_node	0.02 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_4002 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4002 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,