RetrogeneDB ID: retro_mdom_1068

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:486995800..486997194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008869
• Aliases: None
• Description: None

Sequence

>retro_mdom_1068
AGTGCATCAGTGGCCCGGCCTCCATCGTCATCGTCACCGCCACAGCTGCTACTACTTCTGCTGGCGCTGTTGCTTGCCAC
TGCCGCCGCGGAGCAGCAGGTGCCGCTGGTGCTCTGGTCAAGCTCTCGGGACTTGTGGGTCCCACTGGAGAATGCCCACG
AAGGGCACATCACCACGGATGGCCAGCTGGCCTCCTACCTGGACCCGGTCCTGGAGAAGGGACCCCGAAATGTGCTGTTG
TTCCTGCAGGAAAAGCTAAGCATTGAAGACTTCACTACATATGGCGGTGTGTTTGGCAGCAAGCAAAACAGTGCTTTCTC
TAATCTGGAGAATGCGCTGGAGTTGGCTCCCTCTTCCTTGATTCTGCCTTCGGTGGACTGGTATGCAGCCAGCACCTTGA
CCTCTTACCTGATGGAGAAGCTAGGAGCTAGTCCCCTCCGTGTAGACCAGGCACCCTGAGGGAGCTGAAGCTCAGCGACA
CCCTTCCTGCTCTGCTACTCCCGAGCCTGCCATACACCACCAGTTCCGGCTTGATGGCCCTGAAAGAAGTGCTCACAGGC
AATGATGAGGTTATTGGGCAAGTGATGAACACCCTCAGGGCAGAAGGTGTGCCCTATACGGCCATACTGACTGCTGTTCG
GCCTTCCCGGGTGATTGGGGACTTGTCGATGGTGTCTGGGGGTCTGGGGCGGCACCTCCTTGGAGAGCATGAGGATTTTA
AGCCTGAGCCACCCCCGTCCCCGCCCCTTCCCCCAGTGAGCTACAATGACACAGAGCCTCGAATCCTCTTTTGGGCCCAG
AATTTCACGGTGGCCTATAACAATGAGTTGAGGGACCTGACTGCACTCACCTTTGGAAACCCAGCCCTCAACCTGAGCAG
CTCCAGCTGGAACAGCTCCTTTGCCCAGCTCGCCATGACTTACGAAAACGTCTTTGGCCCACTCCTGACAATCAAGCTCA
TCCTGAACAATCGCTTGTACCCCGTTTCGGCCCGGAATTGGTTCACCATGGACCACCTAGAAATCCACGTCAACAACTCG
GTGGTTGTCTTCAATTCATCCCACATCACAGCACCCAGCATCTATTCCTTCCACTGCGAGTACGTTAGCACGGAACGGTC
CAAGAATAGCCTCCTGGTGGCTTTGCCCAGCTCCTCCGCCTGGCACGTGACTTTCCAGGATTTCCAGATTCAGGCCTTCA
ACCTGTCCAGTGGGAACTTCTCGTATGCCAGCGACTGCGCCAGCTTCTTCTCCCCTGGCATCTGGATGGGGCTGGTCTCC
TCCCTCATCATGCTCTTCATCTTCACCTATGGGCTGCACATGATCCTCCACCTCAAGACCATGGACCGCTTCGATGACCA
CAAGGGGAGCACCCTCTCCGTGCCCCTGACCGAG

Alignment

ORF - retro_mdom_1068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.98 %
• Parental protein coverage: 95.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASSPSSPPPPPPPPQLLLLLLALLLAAAATAAEQQVPLVLWSSSRDLWVPLENAHEGHITTDGQLASYLD
          ..S...PP....PPQLLLLLLALLLA.AA..AEQQVPLVLWSSSRDLWVPLENAHEGHITTDGQLASYLD
Retrocopy SASVARPPSSSSPPQLLLLLLALLLATAA--AEQQVPLVLWSSSRDLWVPLENAHEGHITTDGQLASYLD

Parental  PALEKGPRNVLLFLQEKLSIEDFTTYGGVFGNKQDSAFSNLENTLDLAPSSLILPSVDWYAASTLTSYLK
          P.LEKGPRNVLLFLQEKLSIEDFTTYGGVFG.KQ.SAFSNLEN.L.LAPSSLILPSVDWYAASTLTSYL.
Retrocopy PVLEKGPRNVLLFLQEKLSIEDFTTYGGVFGSKQNSAFSNLENALELAPSSLILPSVDWYAASTLTSYLM

Parental  EKLGASPLHVDQA-TLRELKLNDSLPALLLLRLPYTTSSGLMAPKEVLTGNDEIIGQVMNTLKAEGVPYT
          EKLGASPL.VDQA.TLRELKL.D.LPALLL..LPYTTSSGLMA.KEVLTGNDE.IGQVMNTL.AEGVPYT
Retrocopy EKLGASPLRVDQA<TLRELKLSDTLPALLLPSLPYTTSSGLMALKEVLTGNDEVIGQVMNTLRAEGVPYT

Parental  AILTAVQPSRVIRDLSSMVSGGLGRHLLGENEDFKPEPSPSLPLPPVSYNDTEPRILFWAQNFTVTYNNE
          AILTAV.PSRVI.DLS.MVSGGLGRHLLGE.EDFKPEP........VSYNDTEPRILFWAQNFTV.YNNE
Retrocopy AILTAVRPSRVIGDLS-MVSGGLGRHLLGEHEDFKPEPXXXXXXXXVSYNDTEPRILFWAQNFTVAYNNE

Parental  LRDLTALTFGNPALNLSSSSWNSSFAQLAMTYENVFGSFLTIKLILNNRLYPVSARSWFTMDRLEIHVNN
          LRDLTALTFGNPALNLSSSSWNSSFAQLAMTYENVFG..LTIKLILNNRLYPVSAR.WFTMD.LEIHVNN
Retrocopy LRDLTALTFGNPALNLSSSSWNSSFAQLAMTYENVFGPLLTIKLILNNRLYPVSARNWFTMDHLEIHVNN

Parental  SVVVFNSSHITAPSIYSFHCEYVSTERSKNSLLVALPGSSAWHVTFQDFQIQAFNLSGGNFSYASDCASF
          SVVVFNSSHITAPSIYSFHCEYVSTERSKNSLLVALP.SSAWHVTFQDFQIQAFNLS.GNFSYASDCASF
Retrocopy SVVVFNSSHITAPSIYSFHCEYVSTERSKNSLLVALPSSSAWHVTFQDFQIQAFNLSSGNFSYASDCASF

Parental  FSPGIWMGLVSSLIMLFIFTYGLHMILNLKTMDRFDDHKGSTLSVPLTE
          FSPGIWMGLVSSLIMLFIFTYGLHMIL.LKTMDRFDDHKGSTLSVPLTE
Retrocopy FSPGIWMGLVSSLIMLFIFTYGLHMILHLKTMDRFDDHKGSTLSVPLTE

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_1068 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1068 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
Monodelphis domestica	ENSMODG00000008869	1 retrocopy	retro_mdom_1068 ,
Mus musculus	ENSMUSG00000019087	1 retrocopy	retro_mmus_1198,
Oryctolagus cuniculus	ENSOCUG00000017631	1 retrocopy	retro_ocun_863,