RetrogeneDB ID: retro_cjac_4197

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:84183321..84184011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1IP1
• Ensembl ID: ENSCJAG00000009967
• Aliases: None
• Description: cyclin B1 interacting protein 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:19437]

Sequence

>retro_cjac_4197
TCTTGTCTGCAGCAACAATCTTTCTAGCTAGATATTGTCCTCACAGAACTCAGTCCATCAGAGGAACATAAAGCTATGGT
ATTGGCAGAACTGCAACCAGAGATGGTGTTGAACACTAGCTCCTGAGCACTATACTTTTGGATATATAATGTACCTTGGG
AGTCTCTCTATCAAGAATGAAATTTCAACAAGCTGAGGGCCATCTGAAACAGATGGAGAAGATATATACTCAGCAAATGC
AGAGCAAGGATACTGAATTAACCTTTATAAAAGGAGAGATCACCTCTGTGAAGTAAGTGCTAAAAGAACACAGTAAGAAT
GTTCACTGATATCTTAAAAAAATGGATGGAGTGCAATTATCAGTATCAAAAGCTCTAAGACCTCTATGATAGCCTGAGGC
TATGAAACATTACTGTTGTTAACCAAGAACATACCTTTGAACCATCCATGATTGCACAGTCTAGTATTTTCGGCTTTCCA
TTAGGGGACAACACCAAGTATCCTTTGGACATTGCACCAGTTTAAAATCTGGATGATGGAGATGGAGATTTTTAGTTCAG
ACCTTTTTTTTCCCTCTGGATGCTCAAAAAGCACCTGAACCAAGCAGCAGCTGTTTTCAGTTTTGCCTCTTTAAGCCACG
AATTAGAGCAGCAACAAGTTTCCAGTAGAGTCATGAAAGTGAAAACAATT

Alignment

ORF - retro_cjac_4197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.24 %
• Parental protein coverage: 82.31 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ACNSTLSGKLDIVRTELSPSEEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSK-AEGHL
          .C....S..LDIV.TELSPSEE.KAMVLA.L.PE.VL..SS.AL.FW.Y.V..E.LYQE.NF.K.AEGHL
Retrocopy SCLQQQSF*LDIVLTELSPSEEHKAMVLAELQPEMVLNTSS*ALYFWIYNVPWESLYQE*NFNK<AEGHL

Parental  KQMEKIYTQQIQSKDVELTSMKGEVTSMKKVLEEYKKK-FSDISEKLMERNRQYQKLQGLYDSLRLRNIA
          KQMEKIYTQQ.QSKD.ELT..KGE.TS.K.VL.E..K..F.DI..K.ME.N.QYQKL..LYDSLRL.NI.
Retrocopy KQMEKIYTQQMQSKDTELTFIKGEITSVK*VLKEHSKN>FTDILKKWMECNYQYQKL*DLYDSLRL*NIT

Parental  VANHEGTLEPPMIAQSGVFGFPLGNNSKFPLDSSPVRNRGDGDGDFQFRP-FF--VGSPTAPEPSNS-FF
          V.N.E.T.EP.MIAQS..FGFPLG.N.K.PLD..PV.N..DGDGDF.FRP.FF.......APEPS.S..F
Retrocopy VVNQEHTFEPSMIAQSSIFGFPLGDNTKYPLDIAPV*NLDDGDGDF*FRP<FFFPLDAQKAPEPSSS>VF

Parental  SFASPSRELEHQQVSSRAFKVKRI
          SFAS.S.ELE.QQVSSR..KVK.I
Retrocopy SFASLSHELEQQQVSSRVMKVKTI

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	3.57 RPM
SRP051959_heart	0.00 RPM	5.05 RPM
SRP051959_kidney	0.00 RPM	2.68 RPM
SRP051959_liver	0.00 RPM	0.97 RPM
SRP051959_lung	0.00 RPM	5.58 RPM
SRP051959_lymph_node	0.00 RPM	7.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.59 RPM
SRP051959_spleen	0.00 RPM	5.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4197 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4197 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2617

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009967	2 retrocopies	retro_cjac_3244, retro_cjac_4197 ,
Homo sapiens	ENSG00000100814	1 retrocopy	retro_hsap_4877,
Gorilla gorilla	ENSGGOG00000004586	1 retrocopy	retro_ggor_3046,
Microcebus murinus	ENSMICG00000000893	2 retrocopies	retro_mmur_1264, retro_mmur_1551,
Macaca mulatta	ENSMMUG00000016251	2 retrocopies	retro_mmul_2617, retro_mmul_371,
Nomascus leucogenys	ENSNLEG00000010636	1 retrocopy	retro_nleu_2556,
Pan troglodytes	ENSPTRG00000006088	1 retrocopy	retro_ptro_3249,
Rattus norvegicus	ENSRNOG00000026056	1 retrocopy	retro_rnor_842,
Ictidomys tridecemlineatus	ENSSTOG00000004394	1 retrocopy	retro_itri_1590,