RetrogeneDB ID: retro_mdom_709

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:171965830..171966742(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFSP2
• Ensembl ID: ENSMODG00000004727
• Aliases: None
• Description: UFM1-specific peptidase 2 [Source:HGNC Symbol;Acc:25640]

Sequence

>retro_mdom_709
ATGGTGATTTCAGATATAACAGATCTGCTTTTCAGAATAAGCAGAGGCCCTGATTTAGTATTTCAGCTAGTGCTGCTGAT
AATATTTCTACAACAAAGGCATGAAAATATGTATTGAGTGACCTTTCAACCAAACATTCATCAATTGCCCTTGTGTTCAA
AATTTGCCACAGTTCAGGACCCAACAGCCCCATGAACACACCTCTAGCAAAACTAACTGACAATTCTGCTTGTAAGGAAA
TAATATGCTTTATTCAATTTGACCAAGAAGAGGATACAAAGCAAAAATTCGCCAAAAAGAAAGATAAAAAATTACAAGGA
GAGCCTCAGATAATAAATATAGATCTCATGCTGGAAATGTCAACTTCTCTAGCGGCGATAGCTCCCTTCATTGAAAGAGA
AAGCAGAGGTCACCACTATGTTAACATGACTTTGCCACTTGATACGGTTATATCTGCAGATCCAGAAGAATCATAGAGAA
TAGTTCAAAGCTGTCTACTAAATTCAATTCACAATCAACTAACTGATACAGAGAAATGCATTTTGAAATACATGAAAGGA
ACTTCTATAGTGGTCCCTGAGCCATTGTATTTTTTGTTGCCAGGAGAAAAAAATCTTGTTACAATTTCATATCCATCAAG
AGTTCCAGATGGTCAGCTGCAATCTTACAGAAAAGAATTGCATGACCTGTACGACCTGCCTCATTATAGACCTTACTTCA
AAAGAGCTAATGCATATCATTTTCCAGATGAACCCCATAAAGATGGACATACATATCAGGAATCCTCATACTCATCTAAA
TCCACTGGATACAAAGTCTGGTATGATTTACATAGTTCATCGCATATATGGTTATCATCATGACATGCAAGATTAGATAG
ATGGCAGTGCTTATAGGTCTCTACAAACTTTG

Alignment

ORF - retro_mdom_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVISDTMDLLFRIRGGLDLAFQL-AATDDITMKKALKYVLSDLSTKLSSNALVFKICHSSVYVWPNSNMN
          MVISD..DLLFRI..G.DL.FQL..A.D.I...KA.KYVLSDLSTK.SS.ALVFKICHSS....PNS.MN
Retrocopy MVISDITDLLFRISRGPDLVFQL<SAADNISTTKA*KYVLSDLSTKHSSIALVFKICHSS---GPNSPMN

Parental  TVPAELTDSSACKEILRFIQFDQEEDTKWKFAKKKDKKLQGQPQIINIDLMLEMSTSLAAVAPIIERESG
          T..A.LTD.SACKEI..FIQFDQEED............LQG.PQIINIDLMLEMSTSLAA.AP.IERES.
Retrocopy TPLAKLTDNSACKEIICFIQFDQEEDXXXXXXXXXXXXLQGEPQIINIDLMLEMSTSLAAIAPFIERESR

Parental  GHHYVNMTLPVDAVISADPEESWEVVRIRLVNSVHNQLTDMERCILKYMKGTSVVVPEPLHFLLPGEKSL
          GHHYVNMTLP.D.VISADPEES...V...L.NS.HNQLTD.E.CILKYMKGTS.VVPEPL.FLLPGEK.L
Retrocopy GHHYVNMTLPLDTVISADPEES*RIVQSCLLNSIHNQLTDTEKCILKYMKGTSIVVPEPLYFLLPGEKNL

Parental  ITISYPSGVPDGQLQSYRKELHDLYHLPHDKPYFKRANAYHFPDE-PYK-DAYIR-PHAHLNPLGAESGM
          .TISYPS.VPDGQLQSYRKELHDLY.LPH..PYFKRANAYHFPDE.P.K.D..IR.PH.HLNPL...SGM
Retrocopy VTISYPSRVPDGQLQSYRKELHDLYDLPHYRPYFKRANAYHFPDE>PIKMDIHIRNPHTHLNPLDTKSGM

Parental  IYTVHGIYGYHHYMQDRIDDSGWGCAYRSLQTI
          IY.VH.IYGYHH.MQD.ID....G.AYRSLQT.
Retrocopy IYIVHRIYGYHHDMQD*ID----GSAYRSLQTL

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_709 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_709 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005943	1 retrocopy	retro_cjac_3122,
Monodelphis domestica	ENSMODG00000004727	1 retrocopy	retro_mdom_709 ,
Otolemur garnettii	ENSOGAG00000014660	1 retrocopy	retro_ogar_1617,