RetrogeneDB ID: retro_cjac_1987

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:7272757..7273408(+)
• Located in intron of: ENSCJAG00000001573

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIP13
• Ensembl ID: ENSCJAG00000003849
• Aliases: None
• Description: None

Sequence

>retro_cjac_1987
CTACTCACCAAACGTAATACTGTGTTTGGTGATTATACATGGATTGAGTTTGAGGAACCTTTTCTGACCAGGAATATGCT
GGTCTCTATTGTTGACACAGAATTAAGGGTTAAAGACTCATAGCTCATTGATTTGAGTGCATGCACTATTGCACTTCACA
TCTTCCAGCAGAGTGAAGATGGCGCAAGCAGTGAAAAGTTGGAGGAAGAGACAGAAGATAAAATTGTGGCAAATCATTGG
GTTCTGCCTGCAGCCAAATTCCATGGGCTTTGGAACAGCTTAGTGTCTGATGTGGAAGTCAAATCACACCTTGATTATGT
GATTACAACCTTACCATTTTCAGACAACAATGTCAACAGTAGCCTCAGCACCTGGAACCAGGTGGTGCTGCTGCTACCTG
GTCCTCCAAGAACTGGAAAAACATTCCTATGTAAAGCATTAGCCCAGAAATTGACAATTAAACTTTCAAGCAGGTGTTGG
TATGGCCAATTAATTGCAATAAATAGCCACAGGCTCTTTTCTAAGTGGTTTTCTGAAAGTGAAAAGCTGGTAACTAAGAC
ATTCCAGAAGATTCAAGATTTGATTGATTATAAAGATGCTTTGGCATTTTTACTGATTGATGAGATGGAAAGTCCCACAG
CCACCCATAAT

Alignment

ORF - retro_cjac_1987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.34 %
• Parental protein coverage: 50.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLSRHNIVFGDYTWAEFDEPFLTRNVQSVSIVDTELKVKDSQPIDLSTCKVVLHIFQLNEDGPSSENLEE
          LL...N.VFGDYTW.EF.EPFLTRN...VSIVDTEL.VKDS..IDLS.C...LHIFQ..EDG.SSE.LEE
Retrocopy LLTKRNTVFGDYTWIEFEEPFLTRNML-VSIVDTELRVKDS*LIDLSACTIALHIFQQSEDGASSEKLEE

Parental  ETENIIAANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKKVNSNLITWNRVV-LLHGPPGT
          ETE..I.ANHWVLPAA.FHGLW.SLV.DVEVKSH.LDYV.TTL.FSD..VNS.L.TWN.VV.LL.GPP.T
Retrocopy ETEDKIVANHWVLPAAKFHGLWNSLVSDVEVKSH-LDYVITTLPFSDNNVNSSLSTWNQVVLLLPGPPRT

Parental  GKTSLCKALAQKLTIRLSNRYQYGQLIEINSHSLFSKWFSESGKLVNKMFQKIQDLIDDKDALVFVLIDE
          GKT.LCKALAQKLTI.LS.R..YGQLI.INSH.LFSKWFSES.KLV.K.FQKIQDLID.KDAL.F.LIDE
Retrocopy GKTFLCKALAQKLTIKLSSRCWYGQLIAINSHRLFSKWFSESEKLVTKTFQKIQDLIDYKDALAFLLIDE

Parental  VESLTAARN
          .ES.TA..N
Retrocopy MESPTATHN

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	0.53 RPM	1.73 RPM
SRP051959_heart	0.44 RPM	0.14 RPM
SRP051959_kidney	0.38 RPM	0.20 RPM
SRP051959_liver	0.19 RPM	0.15 RPM
SRP051959_lung	0.36 RPM	0.34 RPM
SRP051959_lymph_node	0.39 RPM	0.71 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.07 RPM
SRP051959_spleen	0.74 RPM	0.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1987 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1987 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1358

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007439	1 retrocopy	retro_chof_2003,
Callithrix jacchus	ENSCJAG00000003849	1 retrocopy	retro_cjac_1987 ,
Dasypus novemcinctus	ENSDNOG00000015202	1 retrocopy	retro_dnov_2464,
Oryctolagus cuniculus	ENSOCUG00000006144	1 retrocopy	retro_ocun_155,
Pongo abelii	ENSPPYG00000015309	1 retrocopy	retro_pabe_1358,