RetrogeneDB ID: retro_cjac_2240

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:70936012..70937129(-)
• Located in intron of: ENSCJAG00000004346

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSCJAG00000013960
• Aliases: None
• Description: None

Sequence

>retro_cjac_2240
AAAAAAAAGAGAGAAAGAAACAAAGCAACCTGTGACACAGTGGGTGATGATAATGAAGAGACCAAAAGAAAATCACCAAA
GAAAAAGGAGAAATATGAATATGAAAAAAAAAAAAGGCCAGGAATCCCAAGTCTTCTAAAGTACAGGCAGTAAAAGACTG
GGCCAGTCAGAGATGTAGTTCTCCAAAAGGCTCTGCTAAAAACAGCGTTGTTAAAGCCAAAAGGAAAGGTGGTGTAAGCA
TTCAGTCAAAGGAGAGTCCCAGTTCCTCCTTGGAGTCTGAGTCTTATCATGAATCAATAGTGATGGTCCCAGCAAAGTCA
CTTTAGAGGCCAGAAATTCCTCAGAAAAATTACCAACTGAGTTATCAAAAGAAGGACCCTCTACCAAAAATACAACTGCA
GACAAACTGGCTACAAAACCTGGCTTTAGCCTTACCCCCAGCAAAGGGAAGACCTCTGGAACATCATCTTCTAGTTCAGA
TTCTGATTCAGAGTCAGATGACCAATGCTTGATGTCATCGAGCTCCCCGGAGTGTGCTGCGGGTTTCTTAAAGACAGGAG
GCCTTTTTGCAGGAAGAGGTTGTCCAGGCCCAGGGCTGTCATCATAGACTGCAGGTGCTGCTGGATGGAAGCGTTCTGGC
TCAAAAGGTGGTAGACAAGTTCCTGGTCCTTTTCCCAATGTGTCTGTCCCCACTAGTTTAGGAAGGGGATGGGGTAGAGG
AGAAAACCTTTTTTCTTGGAAGGGAGCTAAGGGACGGAGCATGTGGGGGAGAGGTCAAGGACGAGGGCATCCTGTCTCTT
GTGTTGTAAATAGAAGCACTGACAACCAGAGGCAACAGCAATTAAACGAAGTGGTAAAAGATTTATCTACTGTTATCCAG
AATCCGGTAGAGACGCACAAGAAGGACTATGGTCTGTTACCACTGTTTGCAGCTGCCCCTAATGTTGGAGAAAAGATTGC
ACTTAAGCTTTTGGAACTAACATCCAGTTACTCTCCTGATTTCTCTGACTACAAGGAAGCAAAAATATTAAGCTGCAATC
CAGAGACCCAACAAGTAGATATAGAAATTATTTGATCCTTACCTGCCTTGAGAGAATCTGGGAAATTTGATTTGGTA

Alignment

ORF - retro_cjac_2240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.12 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKKRRKNKVTGGTVGDDNKETKRKPP--KKKEKCEYKK-KAKNPKSPQVQAVKDWANQRCSSPKGSARNS
          .KKR..NK.T..TVGDDN.ETKRK.P..K.K...E.KK.KA.NPKS..VQAVKDWA.QRCSSPKGSA.NS
Retrocopy KKKRERNKATCDTVGDDNEETKRKSPKKKEKYEYEKKK<KARNPKSSKVQAVKDWASQRCSSPKGSAKNS

Parental  LVKAKRKGGVNVRSKESPSFSSESESCHESI-SDGPSKVTLEARNSSEKLPTELSKEGPSTGNRTADKLA
          .VKAKRKGGV...SKESPS.S.ESES.HESI.SDGPSKVTLEARNSSEKLPTELSKEGPST.N.TADKLA
Retrocopy VVKAKRKGGVSIQSKESPSSSLESESYHESI<SDGPSKVTLEARNSSEKLPTELSKEGPSTKNTTADKLA

Parental  TKPGFSLTPSKGKKTSGTSSSSSDSSSESDDQC--SLSTPECAAGFLKTVGVFAERGCLGPGLLSQTAGA
          TKPGFSLTPSKGK.TSGTSSSSSDS.SESDDQC..S.S.PECAAGFLKT.G.FA.RGC.GPGL.S.TAGA
Retrocopy TKPGFSLTPSKGK-TSGTSSSSSDSDSESDDQCLMSSSSPECAAGFLKTGGLFAGRGCPGPGLSS*TAGA

Parental  AGWKRSGSDGGGQAPGPSPSMSLPTSLGRGWGRGENLFSWKGARGRGMRGRGRGRGHPVSCVMNRSTDNQ
          AGWKRSGS.GG.Q.PGP.P..S.PTSLGRGWGRGENLFSWKGA.GR.M.GRG.GRGHPVSCV.NRSTDNQ
Retrocopy AGWKRSGSKGGRQVPGPFPNVSVPTSLGRGWGRGENLFSWKGAKGRSMWGRGQGRGHPVSCVVNRSTDNQ

Parental  RQQQLNEVVTNSSTIIQNPVDTH-KDYSLLPLLAAAPQVGEKIAFKLLELTSSYSPDVSDYKEGKILSHN
          RQQQLNEVV...ST.IQNPV.TH.KDY.LLPL.AAAP.VGEKIA.KLLELTSSYSPD.SDYKE.KILS.N
Retrocopy RQQQLNEVVKDLSTVIQNPVETHKKDYGLLPLFAAAPNVGEKIALKLLELTSSYSPDFSDYKEAKILSCN

Parental  PETQQVDIEILSSLPALREPGKFDLV
          PETQQVDIEI..SLPALRE.GKFDLV
Retrocopy PETQQVDIEII*SLPALRESGKFDLV

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	0.31 RPM	5.04 RPM
SRP051959_heart	0.23 RPM	5.56 RPM
SRP051959_kidney	0.16 RPM	6.30 RPM
SRP051959_liver	0.11 RPM	4.48 RPM
SRP051959_lung	0.37 RPM	7.55 RPM
SRP051959_lymph_node	0.32 RPM	9.29 RPM
SRP051959_skeletal_muscle	0.26 RPM	4.96 RPM
SRP051959_spleen	0.44 RPM	7.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2240 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2240 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240 ,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,