RetrogeneDB ID: retro_cjac_768

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:27500976..27501449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP9
• Ensembl ID: ENSCJAG00000005170
• Aliases: None
• Description: retinoblastoma binding protein 9 [Source:HGNC Symbol;Acc:9892]

Sequence

>retro_cjac_768
AAGTTTCTGGAGCAGATACCTGGTTTCCAGTGTTTGGCTAAAAACATGCCACACTCAATTACAGCAAGAGAGAGCATCTG
GCTGCCCTTCATGGAGGTGGGGCTGCACTGTGATGAGAAGACCATCATCAACATCCACAGTGCTGGGGCCGTCGCAGCCA
TTAGGTATGCAGAAACACATGAAGTATATGCTATTGTATTCGTGTCTGCATACATATCAGACTTGGGGATGAAAATAAGT
GTGTAAGTGAATACTTCAACTGCCCCTGGCAGTGGGAGAAGATCGGGGCCAGCTACCCTCACATTGTGTAGTTTGGCGCC
ACTGATGACCCATTCCTTCGCTGGAAGGAACAACACGAAGTAGCCGATAGGTTGGAAACCAAATTGTACAAATTCACTAA
CTGTGGCCACTTACAGAACACAGAGTTTCATGAACTGATTACTATGGTAAAGTTTTTGCTAAAAGTACCAGCA

Alignment

ORF - retro_cjac_768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 84.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KELEKIPGFQCLAKNMPDPITARESIWLPFMETELHCDEKTIIIGHSSGAIAAMRYAETHRVYAIVLVSA
          K.LE.IPGFQCLAKNMP..ITARESIWLPFME..LHCDEKTII..HS.GA.AA.RYAETH.VYAIV.VSA
Retrocopy KFLEQIPGFQCLAKNMPHSITARESIWLPFMEVGLHCDEKTIINIHSAGAVAAIRYAETHEVYAIVFVSA

Parental  YTSDLG-DENERASGYFSRPWQWEKIKANCPYIVQFGSTDDPFLPWKEQQEVADRLETKLHKFTNRGHFQ
          Y.SDLG.DEN...S.YF..PWQWEKI.A..P.IV.FG.TDDPFL.WKEQ.EVADRLETKL.KFTN.GH.Q
Retrocopy YISDLG<DENKCVSEYFNCPWQWEKIGASYPHIV*FGATDDPFLRWKEQHEVADRLETKLYKFTNCGHLQ

Parental  NTEFHELITVVKSLLKVPA
          NTEFHELIT.VK.LLKVPA
Retrocopy NTEFHELITMVKFLLKVPA

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	0.02 RPM	1.82 RPM
SRP051959_heart	0.14 RPM	1.86 RPM
SRP051959_kidney	0.09 RPM	4.61 RPM
SRP051959_liver	0.09 RPM	9.08 RPM
SRP051959_lung	0.08 RPM	2.36 RPM
SRP051959_lymph_node	0.02 RPM	2.40 RPM
SRP051959_skeletal_muscle	0.22 RPM	1.35 RPM
SRP051959_spleen	0.08 RPM	2.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_768 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_768 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_768 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013286	1 retrocopy	retro_chof_1398,
Callithrix jacchus	ENSCJAG00000005170	1 retrocopy	retro_cjac_768 ,
Macaca mulatta	ENSMMUG00000004146	1 retrocopy	retro_mmul_2604,
Rattus norvegicus	ENSRNOG00000007972	1 retrocopy	retro_rnor_1118,