RetrogeneDB ID: retro_cjac_1215

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:61638966..61639595(+)
• 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_1215
GCACAACCCAGTGGGCCAGCCGGTGGGAACAAGATCTGTCAGTTTAAGCTGGTTCTGCTGGGGGAGTCTGCAGTGGGCAA
ATCCAGCCTGGTCCTCTGCTTCATCAAGGGACAGTTTCACGAGTACCAGGAGAGCAGAGAGCACCATCAGAGCAGCCTTC
CTCACATAGACTGTCTGCTCCGATGACACAGCAGCCAAGTTGAGATTTGAGACAGCTGGACAGGAGCGATATCACAGCCT
GGCCGCCACGTACTAAGGAGGGGGGCAGGCTGCCATTGTGGTCTATGGCATCACCAACACAGATACATTTGCATGGGCCA
GGAACTGGGTGAAGGAGCTACAGAGGCAGGCCAGCCCCAACATCCTCATTGCACTTGCGGGTAACAAGGCAGACCTGACC
AGCAAGAGAGGCATGGAATTCCAGGAAGCACAAGCCTGTGCAGACGACAGTACTTTGCTGTTGATGTAGACATCAGCAGA
CTGCAACAAATGTGAATGAAATTTTCATGACAATAGCTAAGAAGCTTCCCAAGTATGAGCCTCAGAATGCAGCTGGTGCT
CCAGGCACAAACCAAGGTGTGGACTCCCAGGAGAACAACCCAGCCAGCCTGAGCCAGTGCTGCAGCAAC

Alignment

ORF - retro_cjac_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.09 %
• Parental protein coverage: 97.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFV-KGQFHEYQESTIGAIAAFLTQSVCLDDTTVKFEI
          A.P.G.....KICQFKLVLLGESAVGKSSLVL.F.....F...........AAFLT..VC.DDT..K...
Retrocopy AQPSGPAGGNKICQFKLVLLGESAVGKSSLVLCFI>RDSFTSTRRAESTIRAAFLT*TVCSDDTAAKLR-

Parental  WDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMV
          ..TAGQERYHSLA..Y..G.QAAIVVY.ITN..TFA.A..WVKELQRQASP.I.IALAGNKADL..KR..
Retrocopy FETAGQERYHSLAATY*GGGQAAIVVYGITNTDTFAWARNWVKELQRQASPNILIALAGNKADLTSKRGM

Parental  EYEEAQAYADDNSLLFMETSA-KTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKSQC
          E..EAQA.A.D.S.L........TA.NVN..F..IAKKLPK.EPQN..GA.G...GVD..E......SQC
Retrocopy EFQEAQACA-DDSTLLLM*TS>QTATNVNEIFMTIAKKLPKYEPQNAAGAPGTNQGVDSQENNPASLSQC

Parental  CSN
          CSN
Retrocopy CSN

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	0.07 RPM	25.36 RPM
SRP051959_heart	0.00 RPM	30.61 RPM
SRP051959_kidney	0.04 RPM	28.09 RPM
SRP051959_liver	0.00 RPM	27.49 RPM
SRP051959_lung	0.03 RPM	35.54 RPM
SRP051959_lymph_node	0.16 RPM	20.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.59 RPM
SRP051959_spleen	0.04 RPM	24.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1215 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1215 has 0 orthologous retrocopies within eutheria group .

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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,