RetrogeneDB ID: retro_cjac_1311

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:99057183..99058341(-)
• Located in intron of: ENSCJAG00000006394

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI
• Ensembl ID: ENSCJAG00000014768
• Aliases: CCNI, cyclin-I
• Description: None

Sequence

>retro_cjac_1311
CAGGCAGATCCAAAGGATATCATGAAGTTTCCAGGGCCTTTGGAAAACCAGAGATTGTCTTTCCTGTTGGAAAAGGCAAT
CTCTAGGGAAGCACAGATGTGGAAGGTGAATGTGCAGAAAATACCTTCAAATCAGAATGTTTCTCCATCCCAGAGAGACG
TAGTAATTCAATGGCTGGCCAAACTCAAATACCAATTCAACCTTTACCCAGAAACATTTGCTCTGGCTAGCAGTCTTTTG
GACAGGTTTTTAGCTACTGTAAAGGCTCATCCAAAATACTTGAGTTGTATTGCCATCAGCTGTTTTTTCCTAGCTGCCAA
GACTGTTGAGGAAGATGAGAGAATTCTAGTACTGAAAGTATTGGCAAGAGACAGTTTCTGTGGATGTTCCTCATCTGAAA
TTTTGAGAATGGAGAGAATTATTCTGGGTAAGTTGAATTGGGATCTTCACACAGCCACACCATTGGATTTTCTTCATATT
TTCCATGCCATTGCAGTGTCAACTTTCAGTTTGCCTCAGTTACTTTTCAGTTTGCCCAAATTGAGCCCATCTCAACATCT
GGCAGTCCTTACCAAGCAACTACTTCACTGTATGGCCTGCAACCAACTTCTGCAATTCAGAGGATCCATGCTTGCTCTGG
CCATGGTTAGTCTGGAAATGGAGAAACTCATTCCTGATTGGCTTTCTCTTACAACTGAACTACTTCAGAAAGCACAGATG
GATAGCTCCCAGTTGATCCATTGTCGGGAGCTTGTGGCACATCACCTTTCTACTCTGTAGTCTTCCCTGCCTCTAAATTC
CGTTTATGTCTACCGTCCCCTCAAGCACACCCTGGTAACCTGTGTCAAAGAAGTGTTCAGATTACATCCCTCCTCTGTCT
CAGGCCCAGACTTCTCCAAGGACAACAGCAAGCCAGAAGTGCCAGTCAGAGGTACAGCAGCCTTTTACCATCATCTCCCA
GCTGCCAATGGGTGCAAGCAGATCTCTACTAAATGCAAAGTAGAGGAAATGGAAGTGGATGGCTTTTACGATGGAATCAA
ACGGTTCTATAATGAAGATAATGTTTCAGAAAATGTGGGTTCTGTGTGTGGCACTGATATATCAAGACAGGAGGGACATG
CTTCTCCTTGTCCACCTTTGCAGCCTGTTTCTGTCATG

Alignment

ORF - retro_cjac_1311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QADPKDIMKFPGPLENQRLSFLLEKAISREAQMWKVNVRKIPSNQNVSPAQRDEVIQWLAKLKYQFNLYP
          QADPKDIMKFPGPLENQRLSFLLEKAISREAQMWKVNV.KIPSNQNVSP.QRD.VIQWLAKLKYQFNLYP
Retrocopy QADPKDIMKFPGPLENQRLSFLLEKAISREAQMWKVNVQKIPSNQNVSPSQRDVVIQWLAKLKYQFNLYP

Parental  ETFALASSLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERI
          ETFALASSLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERI.VLKVLARDSFCGCSSSEILRMERI
Retrocopy ETFALASSLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERILVLKVLARDSFCGCSSSEILRMERI

Parental  ILDKLNWDLHTATPLDFLHIFHAIAVST--RPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSM
          IL.KLNWDLHTATPLDFLHIFHAIAVST...PQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSM
Retrocopy ILGKLNWDLHTATPLDFLHIFHAIAVSTFSLPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSM

Parental  LALAMVSLEMEKLIPDWLSLTIELLQKAQMDSSQLIHCRELVAHHLSTLQSSLPLNSVYVYRPLKHTLVT
          LALAMVSLEMEKLIPDWLSLT.ELLQKAQMDSSQLIHCRELVAHHLSTL.SSLPLNSVYVYRPLKHTLVT
Retrocopy LALAMVSLEMEKLIPDWLSLTTELLQKAQMDSSQLIHCRELVAHHLSTL*SSLPLNSVYVYRPLKHTLVT

Parental  CDKGVFRLHPSSVSGPDFSKDNSKPEVPVRGTAAFYHHLPAANGCKQISAKRKVEEMEVDDFYDGIKRLY
          C.K.VFRLHPSSVSGPDFSKDNSKPEVPVRGTAAFYHHLPAANGCKQIS.K.KVEEMEVD.FYDGIKR.Y
Retrocopy CVKEVFRLHPSSVSGPDFSKDNSKPEVPVRGTAAFYHHLPAANGCKQISTKCKVEEMEVDGFYDGIKRFY

Parental  NEDNVSENVGCVCGTDISRQEGHASPCPPLQPVSVM
          NEDNVSENVG.VCGTDISRQEGHASPCPPLQPVSVM
Retrocopy NEDNVSENVGSVCGTDISRQEGHASPCPPLQPVSVM

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	2.44 RPM	22.30 RPM
SRP051959_heart	2.12 RPM	42.36 RPM
SRP051959_kidney	1.38 RPM	29.71 RPM
SRP051959_liver	0.82 RPM	4.94 RPM
SRP051959_lung	1.81 RPM	30.79 RPM
SRP051959_lymph_node	1.62 RPM	26.32 RPM
SRP051959_skeletal_muscle	1.22 RPM	34.79 RPM
SRP051959_spleen	1.47 RPM	32.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1311 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013222	1 retrocopy	retro_cjac_3834,
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311 ,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,