RetrogeneDB ID: retro_mdom_753

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:331292188..331293292(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018476
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DHPS
• Ensembl ID: ENSMODG00000006807
• Aliases: None
• Description: deoxyhypusine synthase [Source:HGNC Symbol;Acc:2869]

Sequence

>retro_mdom_753
GAGGAGGGGCCTGGGTCGCGACCACCCCTGGGAGCCATGGCCACTGTCCTAAGGCACAGCTTGGCGCTGCCCGCGGGGAC
CATCCAGGTCCAGGGCTATGACTTCAACCGCGACCTGGACTATGGCACTCTTCTGAGTGCCTTCGGCACCACGGGCTTTC
AAGCCACCAGCTTCGGCCGCGCAGTACAGCAGGTCAACGCCATGATTGAAAAGAAGCTAGAGCCTCTTGGGGAGGAGGAG
GAGAACCACATGGACCTGAATCCAAGCTGTTGGCCACTGAGTGGCTGCACTATCTTCTTGGGCTACACATCAAATCTAAT
CAGCTCTGGTGTCCGAGAGACCATATGTTACCTGGTACAGCACAACATGGTGGATGATCTGGTGACAACTGCTGGTGTTA
TAGAGGAGGATCTGATCAAATGCCTGGCATCTAAATATCTGGGAGAATTTAGCCTGAAGGGGAAGGACCTGAGACAAAAT
GGCATCAACAGGATTGGAAACTTACTTGTCCCCAATGACAATTACTGCAAGTTTGAGGACTGGTTGATGCCGATTTTGGA
TCAGATGGTTCTGGAGCAAAATACAGAGGGAGTGAAATGGACTCCATCAAAGATGATTGCCCGACTGGGCAAAGAAATCA
ACAACCCTGAATCTGTGTATTACTGGGCACAGAAGAACAACATCCCAGTGCTAAGCCCAGCTCTTACAGATGGCTCTCTT
GGAGATATGATATTCTTCCACTCATATAAGAACCCAGGGCTGGTACTGGACATTGTGGAGGATTTACGACTCATCAATGC
TCAGGCCATCTTTGCCAAGCAAACAGGCATGATTATTCTTGGAGGCGGCCTTGTGAAACACCATATTGGCAATGCTAACC
TCATGAGGAATGGAGCTGATTATGCTGTCTATATCAATATGGCTCAGGAATTTGATGGCTCAGACTCAGGTGCAAGGCCA
GATGAAGCTGTGTCCTGGGGCAAAATCAGAATGGATGCGAGGCCAGTCAAGGTCTATGCTGATGCTTCTCTTGTTTTCCC
TCTGCCTGTGGCAGAGACTATTGCCCAGAAAATTGGGGCCTTCACCACTGAGAAAAAAATTGAC

Alignment

ORF - retro_mdom_753 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.02 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEGPGSRPPPGAVAAVLRHSSALPAGTVQVRGYDFNRGLDYGALLRAFGTTGFQATSFGRAVQQVNAMIE
          EEGPGSRPP.GA.A.VLRHS.ALPAGT.QV.GYDFNR.LDYG.LL.AFGTTGFQATSFGRAVQQVNAMIE
Retrocopy EEGPGSRPPLGAMATVLRHSLALPAGTIQVQGYDFNRDLDYGTLLSAFGTTGFQATSFGRAVQQVNAMIE

Parental  KKLEPLGEEEENHMDLNPSRRPMSGCTIFLGYTSNLISSGVRETIRYLVQHNMVDVLVTTAGGIEEDLIK
          KKLEPLGEEEENHMDLNPS..P.SGCTIFLGYTSNLISSGVRETI.YLVQHNMVD.LVTTAG.IEEDLIK
Retrocopy KKLEPLGEEEENHMDLNPSCWPLSGCTIFLGYTSNLISSGVRETICYLVQHNMVDDLVTTAGVIEEDLIK

Parental  CLAPTYLGEFSLKGKDLRQNGINRIGNLLVPNDNYCKFEDWLMPILDQMVLEQNTEGVKWTPSKMIARLG
          CLA..YLGEFSLKGKDLRQNGINRIGNLLVPNDNYCKFEDWLMPILDQMVLEQNTEGVKWTPSKMIARLG
Retrocopy CLASKYLGEFSLKGKDLRQNGINRIGNLLVPNDNYCKFEDWLMPILDQMVLEQNTEGVKWTPSKMIARLG

Parental  KEINNPESVYYWAQKNNIPVLSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINAQAIFAKRTGMIIL
          KEINNPESVYYWAQKNNIPVLSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINAQAIFAK.TGMIIL
Retrocopy KEINNPESVYYWAQKNNIPVLSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINAQAIFAKQTGMIIL

Parental  GGGLVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRMDARPVKVYADASLVFPLLV
          GGGLVKHHI.NANLMRNGADYAVYIN.AQEFDGSDSGARPDEAVSWGKIRMDARPVKVYADASLVFPL.V
Retrocopy GGGLVKHHIGNANLMRNGADYAVYINMAQEFDGSDSGARPDEAVSWGKIRMDARPVKVYADASLVFPLPV

Parental  AETFAQKIGAFTTEKKID
          AET.AQKIGAFTTEKKID
Retrocopy AETIAQKIGAFTTEKKID

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_753 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_753 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000000465	1 retrocopy	retro_fcat_1573,
Monodelphis domestica	ENSMODG00000006807	2 retrocopies	retro_mdom_731, retro_mdom_753 ,
Sarcophilus harrisii	ENSSHAG00000015920	1 retrocopy	retro_shar_774,