RetrogeneDB ID: retro_cjac_430

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81085211..81085825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51
• Ensembl ID: ENSCJAG00000020821
• Aliases: None
• Description: RAD51 recombinase [Source:HGNC Symbol;Acc:9817]

Sequence

>retro_cjac_430
GCTTCTTCTTCAGTGGAAGAAGAAAAGTCTGGCCTACAACCCATTTCACGGTTAGAACAGTGTGGCATAAATGCCAATGA
TGTGAAAAAAATCGGAAGAAGCTGGATTCCATACTGTGGAGACTGTTGCCTATGCACCAAAGAAGGAGCTAATAAATACG
AGGGGTATCAGGAAGCCAAAGCTGATACAATTCTGGCTGAAGCAGCTAAATTAGTTCCAGCAGGTTTCAGCATGCAACTG
AATTCCACCAAAGGCGGCCAGAGATCACACAGATCACTACTGGCTCCAAAGAGTTTGACAAACTACTTCAAGGTAGAATT
AAGACTGGATGGATCACAGAAACATTTGGAGCATTCCGAACTGGGAAGACCCAGATCTGTCACACATACACTGGCTGTCA
CCTGCCAGCTTCCCATTGACCGAGGTGGAGGTGAAGGAAAGGCCACGTACATTGACACCAAGGGTACTTTAGGGCAGAAA
GGCTGCTAGCAGTGGCTGAGAGGTATAGTCTCTCTGGCAGTGATGTCCTGCATAATGCAGCATACGCTCAAGCATTCAAC
ACAGACTGCCAGACCCAGCTCCTTTATCAAGCATCAGCCACGATAGGAGAATCA

Alignment

ORF - retro_cjac_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ADTSVEEESFGPQPVSRLEQCGINANDVKKL-EEAGFHTVEAVAYAPKKELINIKGI-SEAKADKILAEA
          A..SVEEE..G.QP.SRLEQCGINANDVKK..EEAGFHTVE.VAYAPKKELIN..GI..EAKAD.ILAEA
Retrocopy ASSSVEEEKSGLQPISRLEQCGINANDVKKI>EEAGFHTVETVAYAPKKELINTRGI<QEAKADTILAEA

Parental  AKLVPMGFTT-ATEFHQRRSEIIQIT-GCKELDNLLQGGIETGSITEMFGEFRT-GKTQ-ICHTLAVTCQ
          AKLVP.GF...ATEFHQRR.EI.QIT.G.KE.D.LLQG.I.TG.ITE.FG.FRT.G......HTLAVTCQ
Retrocopy AKLVPAGFSM<ATEFHQRRPEITQITTGSKEFDKLLQGRIKTGWITETFGAFRT>GRPRSVTHTLAVTCQ

Parental  LPIDRGGGEGKAMYIDTEGT-FRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVES
          LPIDRGGGEGKA.YIDT.GT.FR.ERLLAVAERY.LSGSDVL.N.AYA.AFNTD.QTQLLYQASA...ES
Retrocopy LPIDRGGGEGKATYIDTKGT<FRAERLLAVAERYSLSGSDVLHNAAYAQAFNTDCQTQLLYQASATIGES

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	2.53 RPM
SRP051959_heart	0.00 RPM	0.32 RPM
SRP051959_kidney	0.00 RPM	0.27 RPM
SRP051959_liver	0.00 RPM	0.37 RPM
SRP051959_lung	0.02 RPM	0.59 RPM
SRP051959_lymph_node	0.00 RPM	1.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.20 RPM
SRP051959_spleen	0.00 RPM	1.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_430 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_430 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_430 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020821	2 retrocopies	retro_cjac_2811, retro_cjac_430 ,
Ornithorhynchus anatinus	ENSOANG00000028534	1 retrocopy	retro_oana_26,
Otolemur garnettii	ENSOGAG00000031397	1 retrocopy	retro_ogar_3425,