RetrogeneDB ID: retro_cjac_3834

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284890.1:11306..11822(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI2
• Ensembl ID: ENSCJAG00000013222
• Aliases: None
• Description: cyclin I family, member 2 [Source:HGNC Symbol;Acc:33869]

Sequence

>retro_cjac_3834
TCACAGGCTCCGCAGCCCAATCCACAGTCCCTCAAACCGCGCAACCTGGAAGGCATCCTCGACGAGTGCCAGCTGCTCCG
CTACTTGCAGTTGGCCCAGGACCACGAGGTGTGCCTGTGGCAGGGCGGCAAACCCCAGCAGGATGAAATCTGCAACGCCT
TTGAGGAAATCGTGCAGTGGCTTCTGCAGCTTTAGAACAACTTATACTTCTCCCAATCTGCTTTTAACCTGGCCCTCACC
ATCTTCAGCCGCCTCCTGATTTCAGTGAAGGTAAAAGAGAAATACCTGCATTGTGCCGCAATTGTTTCCTCGAGGCTTGC
TGCAAAACTTAATGAAGAAAATGAGGTAATTCCACAAGTAAACCACTTTATAAAGCACCATGGCTCTGACTATTCCCCGG
ATGAGCTGCTGAGGATGGAGCTGGCCATTCTGGACACATTGCACTGGGACCTCTATTTTGGGATGTCACTAGACTTCTTG
ACTGTATTTCATGCCCTGGTGGTCCTGAGCTGGCCG

Alignment

ORF - retro_cjac_3834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 63.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQAPQPDPQSLKPRNLEGILDECQLLRYLHLAQDREARQWQGCKPQ-DEICNAFEEVVQWLLQLQNNLYF
          .QAPQP.PQSLKPRNLEGILDECQLLRYL.LAQD.E...WQG.KPQ.DEICNAFEE.VQWLLQL.NNLYF
Retrocopy SQAPQPNPQSLKPRNLEGILDECQLLRYLQLAQDHEVCLWQGGKPQQDEICNAFEEIVQWLLQL*NNLYF

Parental  SQSTFNLALTIFSRLLISVKVKDKYLHCAAIVSLRLAAKLNEENEVMPQ--DFIKHYGSDYSPNELLRME
          SQS.FNLALTIFSRLLISVKVK.KYLHCAAIVS.RLAAKLNEENEV.PQ...FIKH.GSDYSP.ELLRME
Retrocopy SQSAFNLALTIFSRLLISVKVKEKYLHCAAIVSSRLAAKLNEENEVIPQVNHFIKHHGSDYSPDELLRME

Parental  LAILDTLHWDLYIGTPLDFLTVVSRRCLKSLP
          LAILDTLHWDLY.G..LDFLTV.......S.P
Retrocopy LAILDTLHWDLYFGMSLDFLTVFHALVVLSWP

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	0.11 RPM	0.64 RPM
SRP051959_heart	0.26 RPM	1.02 RPM
SRP051959_kidney	0.11 RPM	0.49 RPM
SRP051959_liver	0.00 RPM	0.13 RPM
SRP051959_lung	0.21 RPM	1.15 RPM
SRP051959_lymph_node	0.07 RPM	0.27 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.37 RPM
SRP051959_spleen	0.08 RPM	0.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3834 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000600	1 retrocopy	retro_chof_1457,
Callithrix jacchus	ENSCJAG00000013222	1 retrocopy	retro_cjac_3834 ,
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Dasypus novemcinctus	ENSDNOG00000001502	1 retrocopy	retro_dnov_2629,