RetrogeneDB ID: retro_cjac_2926

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:105668310..105668847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32E
• Ensembl ID: ENSCJAG00000009710
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member E [Source:HGNC Symbol;Acc:16673]

Sequence

>retro_cjac_2926
ATGAAGATGAAGAAGAAGATTAACCTGGAGTTAAGGAACAGAGCCCCGGAGGAGGTGACAGAGTTAGTCCTTTTTAACTG
CCTGTGTGTTAATGGGGAAATTGAAGGCCTGAATGATACTTTCAAAGAACTAGAATTTCTGAGTATGGCTAATGTGGAAC
TAAGTTCACTGGCCCAGCTTCCCAGCTTAAATAAACTTCGAAAATTGGAGCTTAGTGACAATATAATTTCTGGAGGATTG
GAAGTCCTGGCAGAGAAATGTCCAAATCTTACCTACCTCAATCTGAATGGAAACAAAATAAAAGATCTCAATACAGTAGA
AGCTCTGCAAAATCTTAAAAATTTAAAAAGTCTTGACCTGTTTAACTGTGAAATCACAAACCTGGAAGATTAGAGAGAAA
GTATTTTTGAACTGCTGCAGCAAATCACATACTTAGATGGATTTGATCAGGAGAATAATGAAGCACCAGACTCTAAAGAG
GAGGATGATGAAGATGATGAGGAAGAGGAAAATGAAGCTGGTCCACCTGAAGGATAT

Alignment

ORF - retro_cjac_2926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 69.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMKKKINLELRNRAPEEVTELVLDNCLCVNGEIEGLNDTFKELEFLSMANVELSSLARLPSLNKLRKLE
          M.MKKKINLELRNRAPEEVTELVL.NCLCVNGEIEGLNDTFKELEFLSMANVELSSLA.LPSLNKLRKLE
Retrocopy MKMKKKINLELRNRAPEEVTELVLFNCLCVNGEIEGLNDTFKELEFLSMANVELSSLAQLPSLNKLRKLE

Parental  LSDNIISGGLEVLAEKCPNLTYLNLSGNKIKDLSTVEALQNLKNLKSLDLFNCEITNLEDYRESIFELLQ
          LSDNIISGGLEVLAEKCPNLTYLNL.GNKIKDL.TVEALQNLKNLKSLDLFNCEITNLED.RESIFELLQ
Retrocopy LSDNIISGGLEVLAEKCPNLTYLNLNGNKIKDLNTVEALQNLKNLKSLDLFNCEITNLED*RESIFELLQ

Parental  QITYLDGFDQEDNEAPDSEEEDDEDGDEDDEEEEENEAGPPEGY
          QITYLDGFDQE.NEAPDS.EEDDED...D.EEE.E..AGPPEGY
Retrocopy QITYLDGFDQENNEAPDSKEEDDED---DEEEENE--AGPPEGY

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	12.65 RPM
SRP051959_heart	0.00 RPM	9.96 RPM
SRP051959_kidney	0.07 RPM	7.99 RPM
SRP051959_liver	0.00 RPM	4.05 RPM
SRP051959_lung	0.00 RPM	15.42 RPM
SRP051959_lymph_node	0.00 RPM	20.75 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.49 RPM
SRP051959_spleen	0.00 RPM	15.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2926 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2926 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926 ,
Dipodomys ordii	ENSDORG00000011690	4 retrocopies	retro_dord_311, retro_dord_358, retro_dord_495, retro_dord_777,
Loxodonta africana	ENSLAFG00000026778	1 retrocopy	retro_lafr_580,
Microcebus murinus	ENSMICG00000015265	1 retrocopy	retro_mmur_115,
Monodelphis domestica	ENSMODG00000027412	2 retrocopies	retro_mdom_1802, retro_mdom_569,
Ochotona princeps	ENSOPRG00000010058	3 retrocopies	retro_opri_1223, retro_opri_52, retro_opri_774,
Ictidomys tridecemlineatus	ENSSTOG00000004170	5 retrocopies	retro_itri_1003, retro_itri_1031, retro_itri_1359, retro_itri_394, retro_itri_955,
Tupaia belangeri	ENSTBEG00000001989	1 retrocopy	retro_tbel_918,