RetrogeneDB ID: retro_cjac_3827

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284810.1:9573..10357(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSCJAG00000005029
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_cjac_3827
GAAGGCAAAGGCTCGGAGCTGCCCTCGGACGGGCGGGCTCGGGAAAAGTCAGCTTTATCGTCTATGAGTATTTAAAGCAC
GTAGGAGCCCAGAAATCTGCACAGGCTCCTTATCCGAGATTAGATGGGAAAAAGACATCACGCTGGGAGAACCGCCTGGG
GTTTTGCACCCGTGGCGGCATTTTGGGACCTTTCCTGGGCAGCTCCTGAAAGGAGAGGCGCTTGTGAACATCCAAGTGAA
GCAAAAGCCTGTCGTGATTCTAGTGCAGCAGCTGCCCCGAGCCCCGTGCTTGGCAACATTCCCCCCAATGATGGGGTGCC
GGGAGGCCCCAGCCCGCCAGGTTTCTTTCAGGGTCCTCCGGGGTCACAGCCCTCGCCGCACGCACAGCCTCCACCTCACA
ATCCTAGCAACATGATGGGACCCCACAGTCAGCCTTTTATGTTACGGAGATATGCAGGCAGCCCCAGGCCCCGGATCAGA
ATGGGAAGCCAGCCTCCGGGAGGGGTTCCTGGGACACAGCCATTGCTGCCCATTTCCATGGATCCCACAGGACAACAAGC
CCACCCCAACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCGAGGCATGGGGCCCATGGGTCCTGGCCCACAGAATT
ACAGCAGCGGCATGAGACCATCACCCAACTCCCTCGGTCCCCCCCATGCCCGGGGTTAACATGGGCCCCGGAGCTGGCAG
GCCCTGGCCCAATCCTAACAGTGCTAACTCGATTCCATACTCCTCCTCATCACCCGGTACCTAT

Alignment

ORF - retro_cjac_3827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.64 %
• Parental protein coverage: 67.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGKGSAVPSDGQAREKLAL-YVYEYLLHVGAQKSAQT-FLSEIRWEKNITLGEPPGFLHSWW-CVFWDLY
          .GKGS..PSDG.AREK.AL..VYEYL.HVGAQKSAQ...LSEIRWEK.ITLGEPPG.LH..W...FWDL.
Retrocopy EGKGSELPSDGRAREKSAL<IVYEYLKHVGAQKSAQA<SLSEIRWEKDITLGEPPGVLHP-W<AAFWDLS

Parental  CAAPERRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNP
          .AAPERR..CEH.SEAKA..D.SAAAAPSPVLGNIPPNDG.PGGP.PPGFFQGPPGSQPSPHAQPPPHNP
Retrocopy WAAPERRGACEHPSEAKACRDSSAAAAPSPVLGNIPPNDGVPGGPSPPGFFQGPPGSQPSPHAQPPPHNP

Parental  SSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQAHPNMGGSMQRMNPPRGMG
          S.MMGPHSQPFM..RYAG.PRP.IRMG.QPPGGVPGTQPLLP.SMDPT.QQAHPNMGGSMQRMNPPRGMG
Retrocopy SNMMGPHSQPFMLRRYAGSPRPRIRMGSQPPGGVPGTQPLLPISMDPTGQQAHPNMGGSMQRMNPPRGMG

Parental  PMGPGPQNYGSGMRPPPNSLG-PAMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTY
          PMGPGPQNY.SGMRP.PNSLG.P.MPG.NMGPGAGRPWPNPNSANSIPYSSSSPGTY
Retrocopy PMGPGPQNYSSGMRPSPNSLG>PPMPGVNMGPGAGRPWPNPNSANSIPYSSSSPGTY

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	7.17 RPM
SRP051959_heart	0.02 RPM	11.00 RPM
SRP051959_kidney	0.00 RPM	8.32 RPM
SRP051959_liver	0.00 RPM	3.55 RPM
SRP051959_lung	0.00 RPM	7.95 RPM
SRP051959_lymph_node	0.00 RPM	5.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.39 RPM
SRP051959_spleen	0.00 RPM	7.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3827 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827 ,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302, retro_hsap_1384, retro_hsap_2155, retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,