RetrogeneDB ID: retro_cjac_2231

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:42919437..42919794(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSCJAG00000000769
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_cjac_2231
GAGAAAGAAAAGAAAAAAAAGCAGAAGAGAAGACATTTAGAAATGAGTTTCCAACAGACAGATCCATGTTGTACTTCTGA
TGCACAGCCACATGCATTTCTCCTCAGTGGACCAGCTTCAACAAGGACTTCATTTGCAGCATCCTCACCATTAAAATAAG
AATAGTCCTTATTTACTCTATGGCAGGTTGAGATGATCTATGAATGTTTGTTGAAAAAATGTGAAGAGAAAGTTTGAGAA
GAATATGAAGAAATATTGAACACAAAACTTGCAGAACACTATGATGCTTTTGTGAAGTTTATAAAGCATGATCAAATGAT
CTGACAATATGAAGAACAGTCTGCTAATTATGTTTCA

Alignment

ORF - retro_cjac_2231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.63 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQEYKRMQKRRHLETSFQQTDPCCTSDAQPHAFLLSGPASPGTSSAASSPLKKEQPLFTLRQVGMICERL
          ..E.K..QKRRHLE.SFQQTDPCCTSDAQPHAFLLSGPAS..TS.AASSPLK.E..LFTL.QV.MI.E.L
Retrocopy EKEKKKKQKRRHLEMSFQQTDPCCTSDAQPHAFLLSGPASTRTSFAASSPLK*E*SLFTLWQVEMIYECL

Parental  LKEREEKVREEYEEILNTKLAEQYDAFVKF-THDQIMRRYGEQPASYVS
          LK..EEKV.EEYEEILNTKLAE.YDAFVKF..HDQ....Y.EQ.A.YVS
Retrocopy LKKCEEKV*EEYEEILNTKLAEHYDAFVKFIKHDQMI*QYEEQSANYVS

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	5.66 RPM
SRP051959_heart	0.02 RPM	8.54 RPM
SRP051959_kidney	0.00 RPM	6.81 RPM
SRP051959_liver	0.00 RPM	3.86 RPM
SRP051959_lung	0.00 RPM	10.95 RPM
SRP051959_lymph_node	0.00 RPM	9.41 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.71 RPM
SRP051959_spleen	0.00 RPM	10.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2231 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231 ,
Callithrix jacchus	ENSCJAG00000002309	3 retrocopies	retro_cjac_1460, retro_cjac_3694, retro_cjac_4071,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,