RetrogeneDB ID: retro_cjac_613

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:128525199..128525928(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007918
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CMBL
• Ensembl ID: ENSCJAG00000009079
• Aliases: None
• Description: None

Sequence

>retro_cjac_613
ATGGCTGACGAAGCTTATCCTTGTCCCTGTGACATTGGCCACAGACTTGAGTATGGAGGGATGGGCCATGAAGTTCAAGT
CGAGCACATCAAGGCATATGTCACCAAATCCCCTGTTGATGGAGGCAAAGCTGTTATTGTCATTCAAGATATATTTGGCT
GGCAGTCGCCTAATATCAGATATATGGCTGACATGATCTCAGGAAATGGTTACACAACCATTGTTCCAGACTTCTTTGTA
GGGCAAGAGCCTTGGGACCCCTCTGATGACTGGTCCATCTTCCCTGAGTGGCTGAAAATGAGAAATGCCTGGAAGATCAT
TAGAGAAATCGATGCTGTTTTGAAGTATCTGAAACAATGTCATGCCCAGAAAATTGGCGTGTGGGTTCTGCTGGGGTGGA
ACTGCTGTCCATCACTTGATGATGAAATACTCAGAATTCAGGACAGGGTTTCTGTCTACGGCATCCTCAAGGATTCTGAA
GACATTTACAATTTAAAGAACACCACCTTGTTCATTTTTGCTGAAAATGATGCTGTGATTCCACTCAAGAACGTATCATT
GCTGACCCAGAAGCTGAAAGAACACTGCAAAGTTGAATATCAAATTAAGACATTTTCTGGGCAGACTCACGGGTTCGTGC
ATCGGAAGAGAGAAGACTGTTCACCTGCAGACATGCCCTACATTGACGAGGCCAGAAGGAATTTAATCGAGTGGCCGAAC
AAGTACATG

Alignment

ORF - retro_cjac_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MANEGYPCPCDIGHRLEYGGMGREVQVEHIKAYVTKSPVDAGKAVIVIQDIFGWQLPNTRYMADMISGNG
          MA.E.YPCPCDIGHRLEYGGMG.EVQVEHIKAYVTKSPVD.GKAVIVIQDIFGWQ.PN.RYMADMISGNG
Retrocopy MADEAYPCPCDIGHRLEYGGMGHEVQVEHIKAYVTKSPVDGGKAVIVIQDIFGWQSPNIRYMADMISGNG

Parental  YTTIVPDFFVGQEPWDPSGDWSIFPEWLKTRNARKIDREIDAVLKYLKQQCHAQKIGL-VG-FCWGGIAV
          YTTIVPDFFVGQEPWDPS.DWSIFPEWLK.RNA.KI.REIDAVLKYLK.QCHAQKIG..VG.FCWGG.AV
Retrocopy YTTIVPDFFVGQEPWDPSDDWSIFPEWLKMRNAWKIIREIDAVLKYLK-QCHAQKIGV<VG<FCWGGTAV

Parental  HNLMMKYSEFRAG-VSVYELISNADINCCYNISNQYINANIRTVFIMKLAEVSLLTQKLKEHCKVEYQIK
          H.LMMKYSEFR.G.VSVY......D....YN..N..............L..VSLLTQKLKEHCKVEYQIK
Retrocopy HHLMMKYSEFRTG<VSVYGILK--DSEDIYNLKNTTLFIFAENDAVIPLKNVSLLTQKLKEHCKVEYQIK

Parental  TFSGQTHGFVHRKREDCSPADKPYIDEARRNLIEWLNKYM
          TFSGQTHGFVHRKREDCSPAD.PYIDEARRNLIEW.NKYM
Retrocopy TFSGQTHGFVHRKREDCSPADMPYIDEARRNLIEWPNKYM

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	0.67 RPM	7.57 RPM
SRP051959_heart	0.25 RPM	1.91 RPM
SRP051959_kidney	0.62 RPM	6.32 RPM
SRP051959_liver	1.21 RPM	17.89 RPM
SRP051959_lung	0.07 RPM	0.65 RPM
SRP051959_lymph_node	0.09 RPM	0.87 RPM
SRP051959_skeletal_muscle	0.33 RPM	2.90 RPM
SRP051959_spleen	0.21 RPM	2.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_613 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_613 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_613 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
Choloepus hoffmanni	ENSCHOG00000009759	1 retrocopy	retro_chof_2582,
Callithrix jacchus	ENSCJAG00000009079	1 retrocopy	retro_cjac_613 ,
Dasypus novemcinctus	ENSDNOG00000024697	2 retrocopies	retro_dnov_1840, retro_dnov_2561,
Microcebus murinus	ENSMICG00000000533	1 retrocopy	retro_mmur_1038,
Otolemur garnettii	ENSOGAG00000016909	1 retrocopy	retro_ogar_2398,
Tupaia belangeri	ENSTBEG00000001698	1 retrocopy	retro_tbel_4449,