RetrogeneDB ID: retro_cjac_586

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:90556574..90557883(-)
• Located in intron of: ENSCJAG00000003268

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSG1
• Ensembl ID: ENSCJAG00000013962
• Aliases: None
• Description: None

Sequence

>retro_cjac_586
AGCGCCTGGGCCACACACTTTGAAAAAGAAGACGTGAAGGTTATTTTCTGGTCAGCTCTGGCCAGAGGCATTCACCTGAA
CGCTGACTCTGAGGAAGAGGTAAACAGAGATGATAGACAAAGCAACACAATTGAGTTTGAAAACTCCAGTTTCGACAAGG
CTGAAATTTCACACAATGAGATCAAACATCTCCCAGCCAGGGACTCTCCTTCACTTAGTGAAAATCCCACTACTGATGAA
GAGGACAGTGAGTATGGGCACTGTCAGGAGGAAGAGGAAGATGACTGGCAGACACGTTCAGAAGAAGACAGTCCTGATGA
AGAGGACTGTGGCCAGGACTGGAAGGAAAGCTATATGACAGATTCTGAGGCTCCGGGCAGGAACACCCCACAGAAGAGAC
AGACACACAACTTTAGCCATCTGGTATCAAAGCAGGAGTTACTAGAGCTTTTTAAGGAGCTACATACCGGGAAGAAGGTG
AAAGATGGGCAACTTACAGTCGGACTGGTGGGCTACCCTAATGTTGGTAAGAGTTCAACAATCAACACCATCATGGGCAA
CAAGAAAGTATCTGTGTCTGCCACACCTGGTCACACGAAGCACTTTCAGACACTCTACGTGGAGCCTGGCCTCTGCCTAT
GTGACTGCCTAGGTTTGGTGATGCCATCTTTTGTGTCCACCAAGGCAGAAATGACTTGCAGCAGAATCCTCCCAATTGAT
CAGATGGGAGATCTCGTTCCACCTGTATCATTAGTTTGCCAGAATATTCTAAGACATGTTTTAGAAGTTACCTATGGGAT
GAATATCATAAAGCCTAGAGAGGATGATGATCCCCACCGACCTCCAACATCAGAAGAACTGTTAACAGCTTATGGATATA
TGCGAGGATTCATGACAGCGCATGGACAGTCAGACCAGCCTCGATCTGCGCACTATATCCTGAAGGACTATGTCAGTGGT
AAGCTGCTGTACTGCCATCCTCCCTCCTGGAAGAGATCCTGTAACTTTTCGGATCAACACCAGTGACTCCTAGAGAGCAA
AACGAATGGTGATGAAATAAAAATGCAGCCAGGCAGAAATAAAAAAAGCAAAGCAGATTAAAAATATAGTTGATAAAACT
TTTTTCCATCAAGAGAATGTGAGAGCTTTGACCAAAGGAGTCCAGGCTGTGATGGGTTACAAGCCCAGGAGCAGGGTATT
GACTGCGGCTACTGTGAGCTCTGAGAATGGGGCAGAGATGCCCTGGAAGAAACATGGCAACAGAAATAAAAAAGAAAAAA
GTCATAGACTCTATAAGCACCTGGAAATG

Alignment

ORF - retro_cjac_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.66 %
• Parental protein coverage: 66.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAWATHFEKEDVKVIFWSALAGGIHLNADSEEEVNRDDRQSNTTEFENSSFDEAEISHSETEHLPARDSP
          SAWATHFEKEDVKVIFWSALA.GIHLNADSEEEVNRDDRQSNT.EFENSSFD.AEISH.E..HLPARDSP
Retrocopy SAWATHFEKEDVKVIFWSALARGIHLNADSEEEVNRDDRQSNTIEFENSSFDKAEISHNEIKHLPARDSP

Parental  SRSENPTTDEDDSEYEDCQEEEEDDWQTCSEEDSPDEEDCGQDWKESCMSDSEAPGRNTPQKRQIHNFSH
          S.SENPTTDE.DSEY..CQEEEEDDWQT.SEEDSPDEEDCGQDWKES.M.DSEAPGRNTPQKRQ.HNFSH
Retrocopy SLSENPTTDEEDSEYGHCQEEEEDDWQTRSEEDSPDEEDCGQDWKESYMTDSEAPGRNTPQKRQTHNFSH

Parental  LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG
          LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG
Retrocopy LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG

Parental  LCLCDCPGLVMPSFVSTKAEMTCSGILPIDQMRDHVPPVSLVCQNIPRHVLEVTYGINIIKPREDEDPHR
          LCLCDC.GLVMPSFVSTKAEMTCS.ILPIDQM.D.VPPVSLVCQNI.RHVLEVTYG.NIIKPRED.DPHR
Retrocopy LCLCDCLGLVMPSFVSTKAEMTCSRILPIDQMGDLVPPVSLVCQNILRHVLEVTYGMNIIKPREDDDPHR

Parental  PATSEELLTAYGYMRGFMTAHGQPDQPRSARYILKDYVSGKLLYCHP-PPGRDPVTFQ-HQHQQLLESKT
          P.TSEELLTAYGYMRGFMTAHGQ.DQPRSA.YILKDYVSGKLLYCHP.PPGRDPVTF...QHQ.LLESKT
Retrocopy PPTSEELLTAYGYMRGFMTAHGQSDQPRSAHYILKDYVSGKLLYCHP>PPGRDPVTFR<DQHQ*LLESKT

Parental  NGDEIKIQPGRN-KKAKQIENIVDETFFHQENVRALTKGVQAVMGYKPESRIVTAATASSENGAGKPWKK
          NGDEIK.QPGRN.KKAKQI.NIVD.TFFHQENVRALTKGVQAVMGYKP.SR..TAAT.SSENGA..PWKK
Retrocopy NGDEIKMQPGRN>KKAKQIKNIVDKTFFHQENVRALTKGVQAVMGYKPRSRVLTAATVSSENGAEMPWKK

Parental  HGNRNKKEKSRRLYKHLDM
          HGNRNKKEKS.RLYKHL.M
Retrocopy HGNRNKKEKSHRLYKHLEM

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	2.80 RPM	15.29 RPM
SRP051959_heart	1.89 RPM	24.63 RPM
SRP051959_kidney	2.35 RPM	55.51 RPM
SRP051959_liver	0.54 RPM	24.50 RPM
SRP051959_lung	2.21 RPM	27.70 RPM
SRP051959_lymph_node	0.87 RPM	24.73 RPM
SRP051959_skeletal_muscle	1.03 RPM	24.92 RPM
SRP051959_spleen	2.69 RPM	26.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_586 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013962	1 retrocopy	retro_cjac_586 ,