RetrogeneDB ID: retro_cjac_1829

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:100851953..100853144(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUFY3
• Ensembl ID: ENSCJAG00000014529
• Aliases: None
• Description: RUN and FYVE domain containing 3 [Source:HGNC Symbol;Acc:30285]

Sequence

>retro_cjac_1829
GGTCTGAATCACACTGATGCCAATTTCTGTATGAAAGGAGAAGACTTGGAATCTCAGGTAGGAGTTATAGATTTTTCAGT
GTATCTCAAGGACAGAACAGCAGTAAAGGTAGTGAAGGAGACAGTCAGATTACTGCAATCCGGACCAGAAGAACTACCTA
GAAGAACTGAACAGATATTTGAATGCTACTGTAAACAACCTTCAGGCAAAAGTAGATGCATTAGAAAAATCGAACACTAA
ACTGACAGGAGCTTGAAGTTGCAAACAACAGGATTATTGCCTTATAAGAAGAAATGGAACAAGTTAAAGAGGAAAGTTCC
TACATACTGGAATCCAATCAGAAGGGTCCCAAGCAAGACAGAACTTCAGAAGGGCAAGCACTAAGTGAAGCAAGAAAGCA
TTTAAAAAAAAGAGACACAATTACAATTGGATGTTGAAAAAGAACTGGAGACGCAGATCAGCATGAAGCAGGAGATGGAA
TTGGCTAAGAAGATGCTGGAGAAGGATGTCTGTGAGAAGCAGGATGCTCTGGTATCTCTTCGGCAGCAGCTGCATGATCT
CAGGGATCTCAACCACGAACTTGCTTTTAAGCTGCAGAGTTCAGACTAAGGAGTAAAACAGAAAAGTGAACTAAACAGTC
TCTTGGAAAATTAATTGATGGCTGCTACCATTAAACAACTAGAACAAAGATTGCACCAGGCTGAGCGAAGCTGCAAGTCT
GCTGAGTTGGACAAGCAGCTCTTCAAACAGGACTTTGAAGACAAGATCAACAGTCTGCAGCTGAAAGTAGAGGATCTCAC
CAGGCAGTGGAACCAGCTTGAATTAGAACTAAAACAGGAAAAAGAAAGATAACAAAATGACAGAAGCATCCCAGGAAAGG
GTTACCAGAAGCCAGAATCTAAGACGGATGGGTAGCACAAAATGCTAGAGGGAAATTTTAAACTAAAAAAGCCCCTGGAA
GAAAGACACAGACTGCAACCCCGCCCTCTGAATGAACAGGGTCAGCTGCTGCGCTCTGAGAAGCCACAGGTGTGTCAGCT
ATTCCAGAAAGACGGCAGCCTAACAAAGAATATGTGTAAGAACTGCAGAGGAACCTTCTGTAGTGCTGCTTAAGCAAATG
AACTGCCTCTTCCTTCAAGTATCAAGCCTGAGTGAGTTTGCAATCCCTGTCACAAGCATCTGATCCACCAG

Alignment

ORF - retro_cjac_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 70.72 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GLNVIDANFCMKGEDLDSQVGVIDFSMYLKDG-NSSKGSEGDGQITAIL-DQKNYVEELNRHLNATVNNL
          GLN..DANFCMKGEDL.SQVGVIDFS.YLKD..NSSKGSEGD.QITAI..DQKNY.EELNR.LNATVNNL
Retrocopy GLNHTDANFCMKGEDLESQVGVIDFSVYLKDR<NSSKGSEGDSQITAIR<DQKNYLEELNRYLNATVNNL

Parental  QAKVDALEKSNTKLT-EELAVANNRIITLQEEMERVK-EESSYILESNRKGPKQDRTAEGQALSEARKHL
          QAKVDALEKSNTKLT...L.................K.EESSYILESN.KGPKQDRT.EGQALSEARKHL
Retrocopy QAKVDALEKSNTKLT<RSLKLQTTGLLPYKKKWNKLK<EESSYILESNQKGPKQDRTSEGQALSEARKHL

Parental  -KEETQLRLDVEKELEMQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSDLG
          .K.ETQL.LDVEKELE.QISM.QEMELA.KMLEKDVCEKQDALVSLRQQL.DLR.L.HELAFKLQSSD.G
Retrocopy >KKETQLQLDVEKELETQISMKQEMELAKKMLEKDVCEKQDALVSLRQQLHDLRDLNHELAFKLQSSD*G

Parental  VKQKSELNSRLEEKTNQMAATIKQLEQRLRQAERSRQSAELDNRLFKQDFGDKINSLQLEVEELTRQRNQ
          VKQKSELNS.LE.....MAATIKQLEQRL.QAERS..SAELD..LFKQDF.DKINSLQL.VE.LTRQ.NQ
Retrocopy VKQKSELNSLLEN*L--MAATIKQLEQRLHQAERSCKSAELDKQLFKQDFEDKINSLQLKVEDLTRQWNQ

Parental  LELELKQEKERRLQNDRSIPGKGSQKPESKMDGKHKMQEENVKLKKSLEESHRLQPHPVDEQDQLLLSEK
          LELELKQEKE.R.QNDRSIPGKG.QKPESK.DG.HKM.E.N.KLKK.LEE.HRLQP.P..EQ.QLL.SEK
Retrocopy LELELKQEKE-R*QNDRSIPGKGYQKPESKTDG*HKMLEGNFKLKKPLEERHRLQPRPLNEQGQLLRSEK

Parental  PQVCQLCQEDDSLRKNVCQNCRGTFCDACSTNELPLPSSIKPERVCNPCHKHLIKQ
          PQVCQL.Q.D.SL.KN.C.NCRGTFC.A...NELPLPSSIKPE.VCNPCHKHLI.Q
Retrocopy PQVCQLFQKDGSLTKNMCKNCRGTFCSAA*ANELPLPSSIKPE*VCNPCHKHLIHQ

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	38.83 RPM
SRP051959_heart	0.00 RPM	44.18 RPM
SRP051959_kidney	0.00 RPM	51.09 RPM
SRP051959_liver	0.00 RPM	74.60 RPM
SRP051959_lung	0.00 RPM	49.21 RPM
SRP051959_lymph_node	0.00 RPM	40.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.95 RPM
SRP051959_spleen	0.04 RPM	55.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1829 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014529	1 retrocopy	retro_cjac_1829 ,
Nomascus leucogenys	ENSNLEG00000007716	1 retrocopy	retro_nleu_959,