RetrogeneDB ID: retro_cjac_3274

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20000434..20001147(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNJ
• Ensembl ID: ENSCJAG00000016259
• Aliases: None
• Description: None

Sequence

>retro_cjac_3274
GTGGAGCTGGAGGAGCAGTGGTGGCGAGGACAACTGACCGCAGACATTCACCAAGTGCTTCGCTACAAGGAGCTGAAGTT
GCTCTCCTCCAAAGGCCAGTCCCCTCAATGAAGTCTCAGACGGTATTTTGCTGACTTGATTGCCATTGTGAGCAATCGCT
TCACACTCTGCCCTTCTGCCTGCCATCTTGCTGTCTGCTTATGGGCATGTTTATGGACCGCTATGACATCTCTATCCAGC
AGCTGCATTTAGTTGCACTTTCCTGCCTGCTTCTAGCAAGTAAATTTGAAGAAAAAGCAGATAGTGTGCCTAAGCTGGAG
CAGCTCAACAGCCTGGGTTGTATGACTAATATGAATCTAGTATTAACAAAACAAAATTTGCTACATATGGAACTATTATT
ATTAGAAACCTTTTGGTAGAACCTCTGCCTTCCGACAGCTGCCCATTTCATTGAGTATTATTATCTCTCTGAAGCAGTAC
ATGGAACAGATCTTCATGACGGCTGGCCAATGATTTGCTTGGAAAAGACTAAACTCTACATGGCCACATACGCAGATTAC
TTCCTGGAAGTATCTTTGCAAGATTATGCCTTTCTAAATTATGCACCTTCTTTAGTAGCTGCTGCATGTGTGGCTTCTTC
GAGGATAATACTTCGTTTTTCTCCAACGTAGCCTACGAGACTACATTGTCTTACTGCTTACTCTTGGGATTTC

Alignment

ORF - retro_cjac_3274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELEGQWWRGQLAADIHQALRYKELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAV-YLLD
          .ELE.QWWRGQL.ADIHQ.LRYKELKL.S.KGQSPQ.SLRRYFADLIAIVSNRFTLCPSA.HLAV..L..
Retrocopy VELEEQWWRGQLTADIHQVLRYKELKLLSSKGQSPQ*SLRRYFADLIAIVSNRFTLCPSACHLAV<LLMG

Parental  LFMDRYDISIQQLHLVALSCLLLASKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFQ
          .FMDRYDISIQQLHLVALSCLLLASKFEEK.DSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETF.
Retrocopy MFMDRYDISIQQLHLVALSCLLLASKFEEKADSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFW

Parental  WNLCLPTAAHFIEYY-LSEAVHETDLHDGWPMICLEKTKLYMAKYADYFLEVSLQDYAFLNYAPSLVAAA
          .NLCLPTAAHFIEYY.LSEAVH.TDLHDGWPMICLEKTKLYMA.YADYFLEVSLQDYAFLNYAPSLVAAA
Retrocopy *NLCLPTAAHFIEYYYLSEAVHGTDLHDGWPMICLEKTKLYMATYADYFLEVSLQDYAFLNYAPSLVAAA

Parental  CVASSRIILRLSPTWPTRLHRLTAYSWDF
          CVASSRIILR.SPT.PTRLH.LTAYSWDF
Retrocopy CVASSRIILRFSPT*PTRLHCLTAYSWDF

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	6.61 RPM
SRP051959_heart	0.00 RPM	6.17 RPM
SRP051959_kidney	0.00 RPM	6.61 RPM
SRP051959_liver	0.00 RPM	4.07 RPM
SRP051959_lung	0.02 RPM	8.26 RPM
SRP051959_lymph_node	0.00 RPM	7.33 RPM
SRP051959_skeletal_muscle	0.04 RPM	6.46 RPM
SRP051959_spleen	0.00 RPM	6.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3274 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3274 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	ENSCJAG00000016259	1 retrocopy	retro_cjac_3274 ,
Erinaceus europaeus	ENSEEUG00000002270	2 retrocopies	retro_eeur_535, retro_eeur_577,
Homo sapiens	ENSG00000107443	1 retrocopy	retro_hsap_3850,
Gorilla gorilla	ENSGGOG00000006034	1 retrocopy	retro_ggor_2595,
Oryctolagus cuniculus	ENSOCUG00000011114	1 retrocopy	retro_ocun_425,
Tarsius syrichta	ENSTSYG00000009466	1 retrocopy	retro_tsyr_741,