RetrogeneDB ID: retro_mdom_1440

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:70926547..70927322(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPSAP1
• Ensembl ID: ENSMODG00000009171
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase-associated protein 1 [Source:HGNC Symbol;Acc:9466]

Sequence

>retro_mdom_1440
CTCCCATCACTGTCATAGAACAAACAAAGCAAAATGAGAAAGAGGGTTTTTATTGTGTGCAATATCCTAGCTTCTATGTT
AGCCAAAGCAGGTTTAACACACATTATAACTATGGATCTTCATCAAATGGAAATATAAGGCTTTTTCAGCTTCCCTGTGG
ACAGCCTCAGAACATCACTTTTCCTACTATGATATATCCAAGAATAAATTTCAAATTACAGAAGTGTAGGCATTGTAGCC
AAGTCTCCTGATGCTGGAAAGAAGGTCCAATCATATCCTGAGAGACTTCACTTGGGTTCAGCTTAGTATATGGAGAGACT
TAATATACAGCGTTCAACATGAATGATGGACATCATTCTCCTCCAAAGGTCAAAAAGGCTACCATCCACCCTAGTGTTGA
GTTGCCTTTGATTATGGCCAAAGAAAACCACCAATTACTGTAGTTGGAGATGTTGGAGGGTCAATTACCATCATAATGGA
CAACATCATTGATGATGTGGAAAGATTTATGGATGCTGCCAACATACTCAAATAGTGAGGTGCCTACAGGATTTATGTCA
TGGCCACTCATGGCATCTTGTCTACAGATGCTCCCCACCTCAGGAAGGAATCTTCCATTGTTGAGCTGACCAACACAGTT
CTTTAAGAGTTACAGAAAATGAAGTGTCCCATAATAAAGGCTGTTAACATTAGTTTGATTTTTTCAGAAGCCATACAAAG
ATTCCATAATGGGGAGTCCATGACCTACTTGTTTAGAGACATTACTGTAGATGAC

Alignment

ORF - retro_mdom_1440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 67.79 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPYFPYSKQSKMRKRGSIVCKLLASMLAKAGLTHIITMDLHQKEIQGFFSFPVDNLRASPFLLQYIQEEI
          .P.....KQSKMRKR..IVC..LASMLAKAGLTHIITMDLHQ.EI.GFFSFPVD.LR.S.FLL.YIQE.I
Retrocopy LPSLS*NKQSKMRKRVFIVCNILASMLAKAGLTHIITMDLHQMEI*GFFSFPVDSLRTSLFLL*YIQE*I

Parental  PNYRNAVIVAKSPDAAKRAQSYAERLRLGLA-VIHGEAQCTELDMDDGRHSPPMVKNATVHPGLELPLMM
          .NYR...IVAKSPDA.K..QSY.ERL.LG.A....GE...T...M.DG.HSPP.VK.AT.HP..ELPL.M
Retrocopy SNYRSVGIVAKSPDAGKKVQSYPERLHLGSA<LVYGET*YTAFNMNDGHHSPPKVKKATIHPSVELPLIM

Parental  AKE-KPPITVVGDVGGRIAIIVDDIIDDVESFVAAAEILKERGAYKIYVMATHGILSADAPRLIEESSID
          AKE.KPPITVVGDVGG.I.II.D.IIDDVE.F..AA.ILK..GAY.IYVMATHGILS.DAP.L..ESSI.
Retrocopy AKE<KPPITVVGDVGGSITIIMDNIIDDVERFMDAANILK**GAYRIYVMATHGILSTDAPHLRKESSI-

Parental  EVVVTNTVPHEVQKLQCPKIKTVDISLILSEAIRRIHNGESMAYLFRNITVDD
          .V..TNTV..E.QK..CP.IK.V.ISLI.SEAI.R.HNGESM.YLFR.ITVDD
Retrocopy -VELTNTVL*ELQKMKCPIIKAVNISLIFSEAIQRFHNGESMTYLFRDITVDD

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	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1440 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1440 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003550	1 retrocopy	retro_dnov_280,
Monodelphis domestica	ENSMODG00000009171	1 retrocopy	retro_mdom_1440 ,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,