RetrogeneDB ID: retro_cjac_1879

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:197695139..197695759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSCJAG00000007527
• Aliases: None
• Description: RAB5B, member RAS oncogene family [Source:HGNC Symbol;Acc:9784]

Sequence

>retro_cjac_1879
ACACCCAGGCCCAATGAGGCCTGCAAAATATGCCAGTTCAAATTTGTCCTGCTGGGATAATCTGCAGTGGGAAAGTCAAG
CCTGGTACTATGTTTTCTCAAAGGGCGGTTCCATGAGCACCAGGAGTGCACCATCGGGGAGGCCTTCCTCACCCAGTCCA
TTTGTCTAGATGCCACAACTGTCAAGTTTGAGATCTGGGACATAGCTGGGCAGAAGCGAAACCACAGCTTAGCCCCCACG
TGCCACAGGGGTGCCCAAGCTGCAATGGTGGTTTATGACATTACTAATCAGAAAACCTTTGCCTGAGCGAAGACATGTGT
GAAGAAACTACAGCGACAGGCCAGTCCTAGCCTCATGATTTCCCTGGCGGTGAACAAAGCTGACCGGCCAATAAGAGTGT
GGTGGAGTATGAAGAGGCCCAGGTCTATGCAGATGAGAACAGCTTATTGTTTATGGAGACTTCAGCCAAGACAGCTATGA
ACAAGAATGATTCCCTCTTAGTAATAGCTAAAAAGTTGCCCAAGAGTGAACCCCAGAATCTGAGAGGCACAGCAGGCTGA
AGCTGGGGTGTGGATCTCCATGAACAGTCCCAGCAGAACAAGAGTCAGTGATGTAGCAGC

Alignment

ORF - retro_cjac_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77. %
• Parental protein coverage: 97.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAIAAFLTQSVCLDDTTVKFEI
          T.RPN....A.KICQFK.VLLG.SAVGKSSLVL.F.KG.FHE.QE.TIG...AFLTQS.CLD.TTVKFEI
Retrocopy TPRPN---EACKICQFKFVLLG*SAVGKSSLVLCFLKGRFHEHQECTIGE--AFLTQSICLDATTVKFEI

Parental  WDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADL-ANKRM
          WD.AGQ.R.HSLAP...RGAQAA.VVYDITNQ.TFA.AKT.VK.LQRQASPS..I.LA.NKAD..ANK..
Retrocopy WDIAGQKRNHSLAPTCHRGAQAAMVVYDITNQKTFA*AKTCVKKLQRQASPSLMISLAVNKADR<ANKSV

Parental  VEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKSQC
          VEYEEAQ.YAD.NSLLFMETSAKTAMN.ND..L.IAKKLPKSEPQNL.G.AG.S.GVDLHEQSQQNKSQ.
Retrocopy VEYEEAQVYADENSLLFMETSAKTAMNKNDSLLVIAKKLPKSEPQNLRGTAG*SWGVDLHEQSQQNKSQ*

Parental  CSN
          CS.
Retrocopy CSS

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	25.36 RPM
SRP051959_heart	0.00 RPM	30.61 RPM
SRP051959_kidney	0.00 RPM	28.09 RPM
SRP051959_liver	0.00 RPM	27.49 RPM
SRP051959_lung	0.00 RPM	35.54 RPM
SRP051959_lymph_node	0.00 RPM	20.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.59 RPM
SRP051959_spleen	0.00 RPM	24.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1879 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1879 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178, retro_cjac_1179,
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879 ,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,