RetrogeneDB ID: retro_cjac_1120

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:107925882..107926512(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8B
• Ensembl ID: ENSCJAG00000015842
• Aliases: None
• Description: ADP-ribosylation factor-like 8B [Source:HGNC Symbol;Acc:25564]

Sequence

>retro_cjac_1120
GCAGAAGCGGCTCACGTGGAAATCATCAATGCCGCCCATGGTCTGCCCTCCCATCAGTCCTTGCTCCCAGCCGCCATCAT
GCTGGTGTTCGTCTCCCGCCTGCTGGACTGATTTCCGTTTACTCTTCTGAAAGGAGGAGATGGAGCTGATGCTCATGAAG
CTGCAGTACTCTGGGAAGAACACCTTCATCAGTGTCATCACATCAGGTCAATTTAGTGAAGATGTGATACCCACAGTGAG
CTTCAACATGAGGAAGATAACTAAAGGTAATGTCACAGTAAAGATCTAGGACACAGGAGGACAACCCGATTTTGAAGCTT
GTGGGGGTATTGCAGAGGAGTCAATGCTATAGTTTACCTGATAGACACTACAGATTGTGAAAAGGTAGAACCTTCCCGAA
ATGAACTACGTAATCTTCTAGATAAATCACAGTAACAAGGAATTCCGCTAGTGCTTGGAAACAAGAGAGATCTTCCTAAT
GCCTTGGATGAGAAACAGCTAATTGAAAAAAATGAATCTGTCTGTTATTCAGGATAGAGAAAATGCTGCCATTCAATTTC
TTGCTAAGAAAAGGATAATATAAATATCACACTTCAGTGGCTTATTCAGCATTCAGAATCTAGAAGAAGC

Alignment

ORF - retro_cjac_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 89.45 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SRCARVEFVDATARPSSRPSSLPAAIMLALISRLLDWF-RSLFWKEEMELTLVGLQYSGKTTFVNVIASG
          ...A.VE...A.....S..S.LPAAIML...SRLLD.F.R.LF.KEEMEL.L..LQYSGK.TF..VI.SG
Retrocopy AEAAHVEIINAAHGLPSHQSLLPAAIMLVFVSRLLD*F>RLLF*KEEMELMLMKLQYSGKNTFISVITSG

Parental  QFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGQP-RFRSMWERYCRGVNAIVYMIDAADREKIEASRNELH
          QFSED.IPTV.FNMRK.TKGNVT.KI.D.GGQP.RF.S.W..YCRGVNAIVY.ID..D.EK.E.SRNEL.
Retrocopy QFSEDVIPTVSFNMRKITKGNVTVKI*DTGGQP<RF*SLW-GYCRGVNAIVYLIDTTDCEKVEPSRNELR

Parental  NLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIE-KMNLSAIQDRE-ICCYSISCKEKDNIDITLQWLIQH
          NLLDK.Q.QGIP.LVLGNKRDLPNALDEKQLIE.KMNLS.IQDRE..CC.SISC.EKDNI.ITLQWLIQH
Retrocopy NLLDKSQ*QGIP-LVLGNKRDLPNALDEKQLIE>KMNLSVIQDRE<KCCHSISC*EKDNINITLQWLIQH

Parental  SKSRRS
          S.SRRS
Retrocopy SESRRS

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	19.15 RPM
SRP051959_heart	0.00 RPM	29.92 RPM
SRP051959_kidney	0.00 RPM	33.77 RPM
SRP051959_liver	0.04 RPM	23.55 RPM
SRP051959_lung	0.00 RPM	26.14 RPM
SRP051959_lymph_node	0.00 RPM	21.32 RPM
SRP051959_skeletal_muscle	0.00 RPM	43.37 RPM
SRP051959_spleen	0.00 RPM	32.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1120 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007757	2 retrocopies	retro_chof_1196, retro_chof_2630,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120 , retro_cjac_470,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Gallus gallus	ENSGALG00000008314	1 retrocopy	retro_ggal_25,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Microcebus murinus	ENSMICG00000000244	2 retrocopies	retro_mmur_1220, retro_mmur_1239,
Mustela putorius furo	ENSMPUG00000017035	2 retrocopies	retro_mputfur_1390, retro_mputfur_541,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343,
Tarsius syrichta	ENSTSYG00000001724	1 retrocopy	retro_tsyr_2150,
Vicugna pacos	ENSVPAG00000012114	2 retrocopies	retro_vpac_495, retro_vpac_519,