RetrogeneDB ID: retro_cjac_1132

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:37609248..37610143(-)
• Located in intron of: ENSCJAG00000006436

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017177
• Aliases: None
• Description: None

Sequence

>retro_cjac_1132
ATGGCTCAGCTAGGAACTCCGAACCTCAATAACGATGTTGTGAAGATGAGAAAAGAAGTGAAGAGAATTCGAGTTTTGAT
TATCCAAAAACTTGTCAGGAGTGTTGGCAGATTGAAGTCAAAAAAGGGTACTGAAGATGCACTGTTGAAAAAGCAAAGAC
GGACGCAACAATTGCTTGAAGAAATCCATGCCATGAGGAAATTGAAACCTGATATGGTAACTAAATCTGTTCTTGGTGAT
GATAACAACTTTGAAAAAATCTGCAAAAAGCCAGATTCTAGTGCAACTGAATGAGCAATTGCCAGACTAGCAGTGCAGCC
TCTTCTGAAGAAAGAGACAGACGTGCTAAAAGCTGCCGTCCAAACCTTTAAAGAGGCAAGACAAAATGTTGCTGAAGTTG
AGTCACCAAGGAATGCTTCCAAGGACAATTATTCTAAGAACACTTGGTATTCAAAAGATAATGGAAGTAATTTACAGCAT
GAAGGAACTATTATCAGTGAGCAAAAAGTGAAAGAAACCAAAATACTGGCAAAGAAACCAGTACTCACTTCAAAGGAAAA
AAATAGCAAGATAGAGCATGAACCTAAAGCAGTGACTATTCCAAATTCTCCATCAAAGCTTTCAGAAAAGGATTCTGTAG
TTTCCTTTGAGTCCCAGAAGACACCTGCTGACCCCAAACTGAAAACACTAAGTCAAACCAAAAAAGGAAAGTATCTGATA
GCTCACTATGTGGTAGCAGTGATGGTAGAGAAGAATTATGTGAAGAGGAGGAGTATTTTGATGATAGCACAGAAGAAAGA
TTTTACAGTCTTCCATGTCTAAAGATAGTGATAGTGGTGATGACTTCTTTACTGGGAAAGTCAGATGGACACGAAGGAAG
GAAAGTAGTTGTCAT

Alignment

ORF - retro_cjac_1132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.9 %
• Parental protein coverage: 70.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALPGTLNLNNEVVKMRKEVKRIRVLVIRKLVRSVGRLKSKKGTEDALLKNQRRAQRLLEEIHAMKELKP
          MA..GT.NLNN.VVKMRKEVKRIRVL.I.KLVRSVGRLKSKKGTEDALLK.QRR.Q.LLEEIHAM..LKP
Retrocopy MAQLGTPNLNNDVVKMRKEVKRIRVLIIQKLVRSVGRLKSKKGTEDALLKKQRRTQQLLEEIHAMRKLKP

Parental  DTVTKSALGDDINLEKICKKPDSTATERAIARLAVHPLLKKKIDVLKAAVQAFKDARQNVAEVESSKNTS
          D.VTKS.LGDD.N.EKICKKPDS.ATE.AIARLAV.PLLKK..DVLKAAVQ.FK.ARQNVAEVES..N.S
Retrocopy DMVTKSVLGDDNNFEKICKKPDSSATE*AIARLAVQPLLKKETDVLKAAVQTFKEARQNVAEVESPRNAS

Parental  EDNHSKNTLYSNDNGNNSQHEGTIISEQKVKETKILAKKPTNNSKEKITKVEHGAKAVTIQNSPSKPSEK
          .DN.SKNT.YS.DNG.N.QHEGTIISEQKVKETKILAKKP...SKEK..K.EH..KAVTI.NSPSK.SEK
Retrocopy KDNYSKNTWYSKDNGSNLQHEGTIISEQKVKETKILAKKPVLTSKEKNSKIEHEPKAVTIPNSPSKLSEK

Parental  NSVVSRESQKTPPDATLKTLSQTK-KTKRSDSSLCGNSDGGEESCEEEREYFDDSTEERFY-KQSSMSED
          .SVVS.ESQKTP.D..LKTLSQTK.K.K.SDSSLCG.SDG.EE.CEEE.EYFDDSTEERFY...S.....
Retrocopy DSVVSFESQKTPADPKLKTLSQTK<KRKVSDSSLCGSSDGREELCEEE-EYFDDSTEERFY<QSSMSKDS

Parental  SDSGDDFFIGKVRRTRKKESSRH
          ....D.FF.GKVR.TR.KESS.H
Retrocopy DSGDD-FFTGKVRWTRRKESSCH

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	0.09 RPM	5.35 RPM
SRP051959_heart	0.04 RPM	5.96 RPM
SRP051959_kidney	0.02 RPM	8.67 RPM
SRP051959_liver	0.04 RPM	7.86 RPM
SRP051959_lung	0.07 RPM	8.38 RPM
SRP051959_lymph_node	0.02 RPM	7.74 RPM
SRP051959_skeletal_muscle	0.04 RPM	6.70 RPM
SRP051959_spleen	0.02 RPM	9.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1132 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1132 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017177	1 retrocopy	retro_cjac_1132 ,
Monodelphis domestica	ENSMODG00000013487	2 retrocopies	retro_mdom_1304, retro_mdom_1705,
Otolemur garnettii	ENSOGAG00000032423	1 retrocopy	retro_ogar_1270,
Tarsius syrichta	ENSTSYG00000006869	1 retrocopy	retro_tsyr_1456,