RetrogeneDB ID: retro_cjac_2753

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:116180344..116181116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LUC7L3
• Ensembl ID: ENSCJAG00000018558
• Aliases: None
• Description: LUC7-like 3 (S. cerevisiae) [Source:HGNC Symbol;Acc:24309]

Sequence

>retro_cjac_2753
GTGGTTTCGGCCACATAATTGTTGGATGAGTTAATGGGCTGGGATGGAAACCTCGCCCCAGACAAGAAGCGCAGCAACAT
GTGGTAGGACCACAAGAGCATTTATAAATATTTTCTCTGTGGTTTTTTTCTGCAGAATTGTTCACAAATACACATTCTGA
TCTCGGTCCATGTGAAAAAAACTCATACTGAAAACCTACAAAAGTAGTATAAGAAGAGCTCTTGTTTTATGAAAGTTGGC
TATGAGAGAGGTTTTTCTTTTCCATAATTACAGAGCTTACTTGCAAAAGTAGAGCATAGAATCAGGTGAGGCCATGCTCG
TTTGGCATCTCAAGACCAGCAGTCTTCTTGGGCGGCTGGCCCAACAGGCAAAAATGAAGCAAAAATTCAGGCTCTAACAG
ACAACACTGATGTGCTTCTGCAACAGATTGAAGAATTAGGGGTGGAAGGAAAAGTAGAAGAAGCCCAGTGGAAGATGAAA
TTAGTTGAACAATTAAAAGAAGAGAGAGAATTGCCTAGATCCACAACCTTGAAATTGAAAGTTTTGCTGAACACATACAA
AAAAAATGGAAGTTGGTGAAGTGTGTGGAGCCTTTTTGATAGTAGGAGATGCCCAGTCCCAGGTAGACGACCGTTTGTTG
GGAAGACAACACATGGGATGTGCCAACATTAAAACTACTGTAGAAGAATTAAAAGAAACATTAAGAAAAAGAACTCAAGA
ACTTAATCATGATGACTGTCTAAAAAGGGAAAAGCAAGAAAGAAAAGAGAAA

Alignment

ORF - retro_cjac_2753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.48 %
• Parental protein coverage: 59.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MISAAQLLDELMGRDRNLAPDEKRSNVRWDHESVCKYYLCGFC-PAELFTNTRSDLGPCEK-IHDENLRK
          ..SA..LLDELMG.D.NLAPD.KRSN...DH.S..KY.LCGF...AELFTNT.SDLGPCEK..H.ENL.K
Retrocopy VVSAT*LLDELMGWDGNLAPDKKRSNMW*DHKSIYKYFLCGFF<SAELFTNTHSDLGPCEK>THTENLQK

Parental  QYEKSSRFMKVGYERDF-LRYLQSLLAEVERRIRRGHARLALSQNQQSSGAAGPTGKNEEKIQVLTDKID
          .Y.KSS.FMKVGYER.F....LQSLLA.VE.RIR.GHARLA.SQ.QQSS.AAGPTGKNE.KIQ.LTD..D
Retrocopy *YKKSSCFMKVGYERGFSFP*LQSLLAKVEHRIR*GHARLA-SQDQQSSWAAGPTGKNEAKIQALTDNTD

Parental  VLLQQIEELGSEGKVEEAQGMMKLVEQLKEERELLRSTT-STIESFAAQ-EKQMEVCE-VCGAFLIVGDA
          VLLQQIEELG.EGKVEEAQ..MKLVEQLKEEREL.RSTT...IESFA....K.......VCGAFLIVGDA
Retrocopy VLLQQIEELGVEGKVEEAQWKMKLVEQLKEERELPRSTT<LEIESFAEHIQKKWKLVK<VCGAFLIVGDA

Parental  QSRVDDHLMGKQHMGYAKIKATVEELKEKLRKRTEEPDRDERLKKEKQEREER
          QS.VDD.L.G.QHMG.A.IK.TVEELKE.LRKRT.E...D..LK.EKQER.E.
Retrocopy QSQVDDRLLGRQHMGCANIKTTVEELKETLRKRTQELNHDDCLKREKQERKEK

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	23.43 RPM
SRP051959_heart	0.02 RPM	55.50 RPM
SRP051959_kidney	0.00 RPM	55.64 RPM
SRP051959_liver	0.00 RPM	30.65 RPM
SRP051959_lung	0.00 RPM	83.31 RPM
SRP051959_lymph_node	0.00 RPM	100.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	51.95 RPM
SRP051959_spleen	0.00 RPM	80.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2753 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2753 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	ENSCJAG00000018558	1 retrocopy	retro_cjac_2753 ,