RetrogeneDB ID: retro_cjac_3244

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:93915522..93916354(+)
• 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_3244
ATGTCTTTGTGTGAAGACATGCTGCTTTGTAATTATCGAAAGTGTCGCATCAAACTCTCTGGCAATGCATGGGTCACTGC
CTGTTCTCACATCTTCTGTGATCAGCATGGCAGTGGTGAATTTAGTCGCTCACTAGTTATCTGTCCTGCCAGCAACAGTA
CCCTTTCTGGAAAGCTAGATATTGTCCGCACAGAACTCAGTCCATCAGAGGAATATAAAACTATGGTACTGGCATGACTG
AGACCAGAGATCGTGTTGGACATTACCTCCTGAGCACTGGCCTTCCGGACATACCAGGTACATCAGGAACGTCTCTATCA
AGAATACAATTTCAGGAAGGCTGAGGGCCACCTGAAACAGATGGAGAAGATATATACTCAGCAAATACAAAGCAAGGATG
TAGAATTGACCTCTATGAAAGGGGAGGTCACCTCCATGGAGACAGTGATAGAAGAATACAAGAAAAAGTTCAGTGACATC
TCTGAGAAACTTATGCAGTGCAGTCGTCAGTATCAAAAGCTCCAAGGCCTCTGTGATAGCCTTTGGCTATGAAACATCAC
TATTGCTAACCATGAAGGCACCCCTGAACCATCTATGATTGCACAGTCTGGTGTTTTTGGCTTCCCATTAGGTAACAACT
CCAAGTTTCCTTTGGATAGTTCACTTGTTCGAAATTGGGGAGATGGAGATGGATATTTTCAGTCCAGACCATTTTTTGTA
GGTTCTCCCACAGCACCTGAACCCAGCAACAGCTTTTTTTAGTTTTGCCTCTCCAAGTCATGAATTAGAGCAGCAGCAAG
TTTCTAGCAGGGCCTTCAAAATAAAAAGAATT

Alignment

ORF - retro_cjac_3244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLCEDMLLCNYRKCRIKLSGYAWVTACSHIFCDQHGSGEFSRSPAICPACNSTLSGKLDIVRTELSPSE
          MSLCEDMLLCNYRKCRIKLSG.AWVTACSHIFCDQHGSGEFSRS..ICPA.NSTLSGKLDIVRTELSPSE
Retrocopy MSLCEDMLLCNYRKCRIKLSGNAWVTACSHIFCDQHGSGEFSRSLVICPASNSTLSGKLDIVRTELSPSE

Parental  EYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQMEKIYTQQIQSKDVELTSMK
          EYK.MVLA.LRPEIVLDI.S.ALAF.TYQVHQERLYQEYNF.KAEGHLKQMEKIYTQQIQSKDVELTSMK
Retrocopy EYKTMVLA*LRPEIVLDITS*ALAFRTYQVHQERLYQEYNFRKAEGHLKQMEKIYTQQIQSKDVELTSMK

Parental  GEVTSMKKVLEEYKKKFSDISEKLMERNRQYQKLQGLYDSLRLRNIAVANHEGTLEPPMIAQSGVFGFPL
          GEVTSM..V.EEYKKKFSDISEKLM...RQYQKLQGL.DSL.L.NI..ANHEGT.EP.MIAQSGVFGFPL
Retrocopy GEVTSMETVIEEYKKKFSDISEKLMQCSRQYQKLQGLCDSLWL*NITIANHEGTPEPSMIAQSGVFGFPL

Parental  GNNSKFPLDSSPVRNRGDGDGDFQFRPFFVGSPTAPEPSNS-FFSFASPSRELEHQQVSSRAFKVKRI
          GNNSKFPLDSS.VRN.GDGDG.FQ.RPFFVGSPTAPEPSNS.FFSFASPS.ELE.QQVSSRAFK.KRI
Retrocopy GNNSKFPLDSSLVRNWGDGDGYFQSRPFFVGSPTAPEPSNS>FFSFASPSHELEQQQVSSRAFKIKRI

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	0.04 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_3244 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3244 has 0 orthologous retrocopies within eutheria group .

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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,