RetrogeneDB ID: retro_mdom_569

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:330566882..330567294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32E
• Ensembl ID: ENSMODG00000027412
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member E [Source:HGNC Symbol;Acc:16673]

Sequence

>retro_mdom_569
CAGTTAGCCCTTGATAACTGTCATTCTGTCAACGAGGAAATTGGGGGGGCTCAATGACACTTTCAAAGAATTAGAATTTC
TGAGCATGGTCAGGGTGGAGCTTCCCTCTCTGGCTCAGCTCCCCAGCTTGAGTAAACTTTGAAAGTTAGAACTTAGTGAT
AATTTTATTTCTGGGGGCCTGGAGGTCCTGGCAGAAAAATGTCTAAATCTCACCTACCTCAATCTGAGTGGCAATAAAAT
CAAAGATCTCAACACAGTAGAAGCTCTGCAAAATCTTAAAAGTTTGAAAAGCCTTGATTTGTTTAACTGTGAGATCATAC
ACCTGCAAGATTATAGAGAAAGTATTTTTGAACTGCTACAACAAATCACATATCTCGATGGATATGATCAGGGAAATAAT
GAAGCCCCGGAC

Alignment

ORF - retro_mdom_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELVLDNCHSVNGEIEG-LNDTFKELEFLSMVRVELTSLAQLPSLSKLRKLELSDNFISGGLEVLAEKCPN
          .L.LDNCHSVN.EI.G.LNDTFKELEFLSMVRVEL.SLAQLPSLSKL.KLELSDNFISGGLEVLAEKC.N
Retrocopy QLALDNCHSVNEEIGG>LNDTFKELEFLSMVRVELPSLAQLPSLSKL*KLELSDNFISGGLEVLAEKCLN

Parental  LTYLNLSGNKIKDLSTVEALQNLKSLKSLDLFNCEITHLQDYRESIFELLQQITYLDGYDQEDNEAPD
          LTYLNLSGNKIKDL.TVEALQNLKSLKSLDLFNCEI.HLQDYRESIFELLQQITYLDGYDQ..NEAPD
Retrocopy LTYLNLSGNKIKDLNTVEALQNLKSLKSLDLFNCEIIHLQDYRESIFELLQQITYLDGYDQGNNEAPD

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	1.31 RPM	0.00 RPM
SRP007412_heart	0.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.98 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_569 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_569 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
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	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
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,