RetrogeneDB ID: retro_cjac_2489

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:158393218..158393734(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011325
• Aliases: None
• Description: None

Sequence

>retro_cjac_2489
TTGGAGAGTGCTCTCCCTGCTGCCAGCTTCCTGGACTGGGTTGGCGCAGACACCGTGGCCTACCTAGCCCTGCGCACCTG
GTACTGGCTCTTCACCGCCCTCAGGGTCAAGGAAGTGGGGAACTAGGCGGGGGTAGGCCCAGGGCTTGGCAAATGGGCAG
TTGTCACAGGTAGTACAGATAAAATTGAAAAATCATATGCAGAAGAGTTAGCAAAGTGTGGAATGAAAGTTGTCCTTATC
AGCAGTTCACAGAATAAACTTGACCAGGTTTCCAGTGAAGTCAAAGAAAAATTCGTAGTGGAGACCAGAACCATTGTTGC
TGACTTTGCATCAGAAGGTATCTATGGTGAAATTAAAACAGGCCTGGCTGGTCTTGAAATTGGCGTCTTAGTGAACAACG
TGGGAATGTCATATGAGTATCCTGAATACTTTCTGGACATTCCTGACTTGGACAATATGATCAAGAAAATGATAAATATT
AACATTCTTTCTGTTTGTGAGACGACACGACCGGTG

Alignment

ORF - retro_cjac_2489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 55.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESALPVAGFLYWVGAGTVAYVALRISYSLFTAFRVWGVGNEAGVGPGLGEWAVVTGSTDGIGKSYAEEL
          .ESALP.A.FL.WVGA.TVAY.ALR..Y.LFTA.RV..VGN.AGVGPGLG.WAVVTGSTD.I.KSYAEEL
Retrocopy LESALPAASFLDWVGADTVAYLALRTWYWLFTALRVKEVGN*AGVGPGLGKWAVVTGSTDKIEKSYAEEL

Parental  AKRGMKVVLISRSQDKLDQVSSEIKEKFKVETRTIAVDFASEDIYNKIETGLAGLEIGVLVNNVGMAYEY
          AK.GMKVVLIS.SQ.KLDQVSSE.KEKF.VETRTI..DFASE.IY..I.TGLAGLEIGVLVNNVGM.YEY
Retrocopy AKCGMKVVLISSSQNKLDQVSSEVKEKFVVETRTIVADFASEGIYGEIKTGLAGLEIGVLVNNVGMSYEY

Parental  PEHFLDIPDLDNVIKKMININILSVCKMTQLV
          PE.FLDIPDLDN.IKKMININILSVC..T..V
Retrocopy PEYFLDIPDLDNMIKKMININILSVCETTRPV

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	46.04 RPM
SRP051959_heart	0.00 RPM	32.19 RPM
SRP051959_kidney	0.00 RPM	101.86 RPM
SRP051959_liver	0.00 RPM	56.14 RPM
SRP051959_lung	0.02 RPM	31.01 RPM
SRP051959_lymph_node	0.00 RPM	26.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.31 RPM
SRP051959_spleen	0.00 RPM	31.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2489 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489 ,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,