RetrogeneDB ID: retro_cjac_3863

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285298.1:4037..5019(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11FIP5
• Ensembl ID: ENSCJAG00000003950
• Aliases: None
• Description: RAB11 family interacting protein 5 (class I) [Source:HGNC Symbol;Acc:24845]

Sequence

>retro_cjac_3863
GGTGCTGCGGGGCAAGACGGCAGCACCAGCGACGCCTACACGGTGATCCAGGTGGGCCGCGACAGTACAGACGTGGGTGG
TGGAAAAGACGCAGGCTGCCCAGAGCGGCGTGAGGACTGCTCATTCCAGCCGCCGCCGGGCGCCCTGGTTGACCTGCTGC
GGGCGCAGGAGGTGGATGCGGGCCAGGCGCCCTGGGCCGCGGGCTCCGCCGCCTGTGAGCTGGTGCTCACACCAGGCACC
GCTCACTCATCCGCGACGGCAAGTTCCTGGGCCAGTCCATGGTGGCGCTGGATGCGGTCTTCTGCGCAGGCTGAGCCGAG
CACACGCAGTGGTACAAACTGCACCCCAAGGCAGGCAAGGAGAAGGAACGTGGCGAGATCGAAGTCACCATCTAGTTCAC
ACGCAAGAGCCGGAGCGCCAGCATGTTTGACCTGTCTGTCCATCAAGGACAAGCCAAGGTCCCGCCTCAGAAAGCAAGAT
CAAGGACAAGATGAAGGGCAAGAAGAAGTATGATCTGGAGTCTGCCTCTGCCATCCTCCCAAGCAGTGCCATAGAGGATC
CTGACCTGGGCAGCCTGGGCAAGATGGGCAAAGCCAAAGACTTCTTCCTCTGCAAGAAGCTGCGCACGTCGTCCCTGACC
CAGTCCAGCACGTCTCTGGGCTCGGACAGCACGCTGTCCTCAGCCAGTGGGAGCCTGGCCTACCAGGGGCCTGGCGCCGA
ACTCCTCACCCGCTCACCGAGCCGCAGCAGCTGGCTGTCCACCGAAGGGGGTGGGGAATCCGCACAGTCCCCCAAGCTGT
TCACCCACAAGAGGACCTACAGCGACGAGGCCAGCCAGATGCGTGCGGCTCCTCCTCGGGCCCTTCTCGACCTTCAGGGC
CACCTGGATGCTGCCTCCCGCTCTTTGCTCCGTGTCAATGGGAACCACATTTACAACTAGGAGCCCCAGGCCCCTGTGCT
TCACCGGGGCTCCATCTTGGGC

Alignment

ORF - retro_cjac_3863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.49 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKSSGAGSTSDAYTVIQV-GREKY-STSVVEKTH-GCPEWREECSFELPPGALDGLLRAQEADEGQAPWA
          G.....GSTSDAYTVIQV.G...Y..T.VVEKT..GCPE.RE.CSF..PPGAL..LLRAQE.D.GQAPWA
Retrocopy GAAGQDGSTSDAYTVIQV<GPRQY<QTWVVEKTQ<GCPERREDCSFQPPPGALVDLLRAQEVDAGQAPWA

Parental  AGSAAACELVLT-TMHRSLIGVDKFLGQATVALDEVFGAGRAQHTQWYKLHSKAGKKEKERGEIEVTIQF
          AGSAA.CELVLT.T.HRSLI...KFLGQ..VALD.VF.AG.A.HTQWYKLH.KAG.KEKERGEIEVTI.F
Retrocopy AGSAA-CELVLT<TRHRSLIRDGKFLGQSMVALDAVFCAG*AEHTQWYKLHPKAG-KEKERGEIEVTI*F

Parental  TRNNLSASMFDLSM-KDKPRSPFSKIKD-KMKGKKKYDLESASA--ILPSSAIEDPDLGSLGKMGKAKGF
          TR...SASMFDLS........P..K....K.K.K.K......SA..ILPSSAIEDPDLGSLGKMGKAK.F
Retrocopy TRKSRSASMFDLSVHQGQAKVPPQKARS<KDKMKGKKKYDLESASAILPSSAIEDPDLGSLGKMGKAKDF

Parental  FLRNKLRKSSLTQSNTSLGSDSTLSSASGSLAYQGPGAELLTRSPSRSSWLSTEGGRESAQSPKLFTHKR
          FL..KLR.SSLTQS.TSLGSDSTLSSASGSLAYQGPGAELLTRSPSRSSWLSTEGG.ESAQSPKLFTHKR
Retrocopy FLCKKLRTSSLTQSSTSLGSDSTLSSASGSLAYQGPGAELLTRSPSRSSWLSTEGGGESAQSPKLFTHKR

Parental  TYSDEASQMRTAPPRALLDLQGHLDAASRSSLCVNGSHIYNEEPQAPVRHRSSISG
          TYSDEASQMR.APPRALLDLQGHLDAASRS.L.VNG.HIYN.EPQAPV.HR.SI.G
Retrocopy TYSDEASQMRAAPPRALLDLQGHLDAASRSLLRVNGNHIYN*EPQAPVLHRGSILG

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	1.38 RPM
SRP051959_heart	0.00 RPM	2.88 RPM
SRP051959_kidney	0.00 RPM	23.12 RPM
SRP051959_liver	0.00 RPM	0.65 RPM
SRP051959_lung	0.00 RPM	2.62 RPM
SRP051959_lymph_node	0.00 RPM	3.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.11 RPM
SRP051959_spleen	0.27 RPM	3.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3863 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3863 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003950	1 retrocopy	retro_cjac_3863 ,