RetrogeneDB ID: retro_cjac_3884

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285806.1:1064..1852(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000714
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCND2
• Ensembl ID: ENSCJAG00000001593
• Aliases: None
• Description: cyclin D2 [Source:HGNC Symbol;Acc:1583]

Sequence

>retro_cjac_3884
CAGCTCCTGTGCTGCGAAGTGGAGGCCATCCGCCGCGCCTACCCCGATGCCAACCTCCTCAACCACCGGGTGCTGCGGGC
CATGCTGAAGGAGGAGGAGACCTGCGCACCCTCCGTGTCCTACTTCAAATGTGTGCAGAAGGAGGTCCTGCCGTCCAGGC
GGAAGATCGTGGCCACCTGGATGCTGGAGGTCTGCGAGGAGCAGAGTGCGAGGAGGAGGTCTTCCCGCTGGCCATGAACT
ACCAGGACCGCTTCCTGTCGCTGGAGCCAGTGAAAAAGAGCCGCCTGCAGCTGCTGGGGGCCACCTGCATGTTCCTCGCC
TCTAAGATGAAGGAGACCATCCCCCTGACGGCCGAGAAGCTGTGCATCTACACCGACAACTCCATCCAACCCGAGGAGCT
GCTGCAAATGGAGCCGCTCCTGGTGAACATGCTCAAGTGGAACCTGGCCGCCATGACCCCGCACGATTTCATCGAACACT
TCCTCTCCAAAATGCCAGAGGCGGAGGAGAACAAACAGATCATCGGCAAACACGCGCAGACCTTCGTTGCCCTCTGCGCC
ACAGATGTGAAGTTCATTTCCTATCCGCCCTCCATGGTGGCGGCGGGAACCGTGGTGGCCGCAGTGCAAGGCCTGAACCT
GGGGAGCCCCAACCACTTCCTGTCCTACTACCGCCTCACCTGCTTCCTCTCCAGAGTGATCAAGTGTGACCCGGACTGCC
TCAGGGCCTGCCAGGAGCAGATCGAAGGCCTGCTGGAGTCGAGCCTGCGCCAGGCCCAGCAGAACCAG

Alignment

ORF - retro_cjac_3884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 91.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELLCCEVDPIRRAVRDRNLLQDDRVLQNLLTIEERYLPQCSYFKCVQKDIQPYMRRMVATWMLEVCEEQ-
          .LLCCEV..IRRA..D.NLL...RVL...L..EE...P..SYFKCVQK...P..R..VATWMLEVCEEQ.
Retrocopy QLLCCEVEAIRRAYPDANLL-NHRVLRAMLKEEETCAPSVSYFKCVQKEVLPSRRKIVATWMLEVCEEQ<

Parental  KCEEEVFPLAMNYLDRFLAGVPTPKSHLQLLGAVCMFLASKLKETSPLTAEKLCIYTDNSIKPQELLEWE
          .CEEEVFPLAMNY.DRFL...P..KS.LQLLGA.CMFLASK.KET.PLTAEKLCIYTDNSI.P.ELL..E
Retrocopy ECEEEVFPLAMNYQDRFLSLEPVKKSRLQLLGATCMFLASKMKETIPLTAEKLCIYTDNSIQPEELLQME

Parental  LVVLGKLKWNLAAVTPHDFIEHILRKLPQQREKLSLIRKHAQTFIALCATDFKFAMYPPSMIATGSVGAA
          ......LKWNLAA.TPHDFIEH.L.K.P...E....I.KHAQTF.ALCATD.KF..YPPSM.A.G.V.AA
Retrocopy PLLVNMLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIGKHAQTFVALCATDVKFISYPPSMVAAGTVVAA

Parental  ICGLQQDEEVSSLTCDALTELLAKITNTDVDCLKACQEQIEAVLLNSLQQYRQDQ
          ..GL........L....LT..L......D.DCL.ACQEQIE..L..SL.Q..Q.Q
Retrocopy VQGLNLGSPNHFLSYYRLTCFLSRVIKCDPDCLRACQEQIEGLLESSLRQAQQNQ

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	3.00 RPM	46.35 RPM
SRP051959_heart	4.77 RPM	15.22 RPM
SRP051959_kidney	7.45 RPM	4.59 RPM
SRP051959_liver	13.06 RPM	3.21 RPM
SRP051959_lung	16.43 RPM	20.95 RPM
SRP051959_lymph_node	2.69 RPM	40.59 RPM
SRP051959_skeletal_muscle	0.76 RPM	1.42 RPM
SRP051959_spleen	6.11 RPM	17.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3884 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884 ,
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Felis catus	ENSFCAG00000000138	1 retrocopy	retro_fcat_809,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
Otolemur garnettii	ENSOGAG00000005208	1 retrocopy	retro_ogar_977,