RetrogeneDB ID: retro_cjac_2199

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:165412127..165413214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM39
• Ensembl ID: ENSCJAG00000017535
• Aliases: None
• Description: None

Sequence

>retro_cjac_2199
GATGAGAACAAGTTAAGCAGTGTCAACAGCCACGAAGAACGTGGCAAAAAGAGGGAAAAAAGCAAGAGCAGAAGTCGTAG
TCATGAACGGAAGAGAAGCAAAAGTAAGGAACGGAAGCAAAGTAGAGATAGAGAAAGGAAAAACAGCAAAAGCCACGAAA
GGAAGCAAAGTAGAAGCAAAGAAAGACGACAGGCTCAAGAAGTCGAGATCGGAGATTTAGAGGCCGCTGCAGAAGTCCTT
ACAGACTACGTTCCCGAAGCAGAAGTCCATTCAGAAAAGGCAAGAGCCCTGTGAGGGAACCTATTGATAATCTAACTCCT
GAGGAAAGAGATGCAAAGACAGTCTTCTGTATGCAGCTGGCAGCAAGAATTCCACCAAGGGATTTGGAAGAGTTTTTCTC
TCCAGCAGGAAAGGTTCCAGATGTGAGGATAATTTCTGACAGAAATTCAAGACGTTCCAAAGGAATTGCTTATGTGGAGT
CTGTTAATGTTAGCTCGGTGCCTCTAGCCATAGGATTAACTGGCCAACGAGTTTGAGGAGTGCCAGTCATAGTACAGGCA
TCACAGGCAGAAAAAAACAGAGCTGCAGCAATGGCAAACAATTTACAAAAGGAAAGTGCTAGACCTATGGGCTGTATGTG
GGTTCATTACACTTTAACAGAACTGCAGATATGCTTAGTGGGATCTTTGAGCCTTTTGGAAGGATTGAAAGTATCCAGCT
GATGATGGACAGTGAAACTGGTCGATCCAGGAGATACGGATTTATTACATTTTCTGATTCAGAATGTGCCAAAAAGGCTT
TGGAACAACTTAATAGATTTGAACTAGCAGGAAGACCAGTGAAAGTTGGTCATGTTACTGAGTGTACTGATGCTTCGAGT
GCTGGTTCATTTTGGGACAGTGATGAACTGGAAAGGACTGGAATTGATTTGGGAACAGTTGGTTATCTTCAGTTAATGGA
AAGACTTGCAGAGGGTACAGGTTTGCAGATTCCACCAGCAGTGCAACAGGCTCTACGAATGAGTGGCTCTTTGGCATTTG
GTGCTGTGGCAGATTTGCAAACAAGACTTTCCCAGCAGACTTGGCTT

Alignment

ORF - retro_cjac_2199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.25 %
• Parental protein coverage: 71.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DENKLSSANGHEERSKKRKKSKSRSRSHERKRSKSKERKRSRDRERKKSKSRERKRSRSKERRRSR-SRS
          DENKLSS.N.HEER.KKR.KSKSRSRSHERKRSKSKERK.SRDRERK.SKS.ERK.SRSKE.RR...SRS
Retrocopy DENKLSSVNSHEERGKKREKSKSRSRSHERKRSKSKERKQSRDRERKNSKSHERKQSRSKE-RRQA<SRS

Parental  RDRRFRGRYRSPYRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGK
          RDRRFRGR.RSPYR.RSRS.SPFRK.KSPVREPIDNLTPEERDA.TVFCMQLAARI.PRDLEEFFS..GK
Retrocopy RDRRFRGRCRSPYRLRSRSRSPFRKGKSPVREPIDNLTPEERDAKTVFCMQLAARIPPRDLEEFFSPAGK

Parental  VRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSAG
          V.DVR.ISDRNSRRSKGIAYVE.V.VSSVPLAIGLTGQRV.GVP.IVQASQAEKNRAAAMANNLQK.SA.
Retrocopy VPDVRIISDRNSRRSKGIAYVESVNVSSVPLAIGLTGQRV*GVPVIVQASQAEKNRAAAMANNLQKESAR

Parental  PM-RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA
          PM..LYVGSLHFN.T.DML.GIFEPFGRIESIQLMMDSETGRS..YGFITFSDSECAKKALEQLN.FELA
Retrocopy PM<GLYVGSLHFNRTADMLSGIFEPFGRIESIQLMMDSETGRSRRYGFITFSDSECAKKALEQLNRFELA

Parental  GRPMKVGHVTERTDASSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAF
          GRP.KVGHVTE.TDASSA.SF.DSDELERTGIDLGT.G.LQLM.RLAEGTGLQIPPA.QQAL.MSGSLAF
Retrocopy GRPVKVGHVTECTDASSAGSFWDSDELERTGIDLGTVGYLQLMERLAEGTGLQIPPAVQQALRMSGSLAF

Parental  GAVAEFSFVIDLQTRL
          GAVA........QT.L
Retrocopy GAVADLQTRLSQQTWL

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	83.69 RPM
SRP051959_heart	0.00 RPM	90.93 RPM
SRP051959_kidney	0.00 RPM	115.68 RPM
SRP051959_liver	0.00 RPM	81.57 RPM
SRP051959_lung	0.00 RPM	141.30 RPM
SRP051959_lymph_node	0.00 RPM	180.31 RPM
SRP051959_skeletal_muscle	0.02 RPM	85.23 RPM
SRP051959_spleen	0.00 RPM	148.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2199 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2199 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008482	1 retrocopy	retro_cjac_1069,
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199 ,
Homo sapiens	ENSG00000131051	1 retrocopy	retro_hsap_4679,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Mus musculus	ENSMUSG00000027620	3 retrocopies	retro_mmus_1512, retro_mmus_2792, retro_mmus_2793,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,
Pongo abelii	ENSPPYG00000010963	1 retrocopy	retro_pabe_3634,