RetrogeneDB ID: retro_mdom_101

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:296802725..296803817(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000014668
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017722
• Aliases: None
• Description: None

Sequence

>retro_mdom_101
ATGGCGGCAGGAGGCGGTGCGGTCCCGAGATGGTCCGCTGGCAGGTGTTCGACGTGGGCCCAAGCTACACCAATCCCACG
CTACACCAATCTCTCGTATATCCAGGAGGGAGCCTATGGCATGGTGTGTTCTGCGTATGACAATGTCAACAAGGTCCGTG
TGGCCATCAAGAAAATCAGCCCCTTTGAGCACCAGACCTACTGCCAGCGGACACTGCTCGAAATCAAGATTTTGCTGCGC
TTCCGCCATGAGAATATCAACCGCATCAACGATATCATTCGGACACCAGCCATCGAGCAGATGAAAGATGTATATATCGT
ACAGGACCTTATGGAAACGGACCTTTACAAGCTCTTGAAGACGCAACACCTCAGCAATGACCACATCTGTTATTTCCCTT
ACCAGATCCTCAGAGGTTTAAAATACATCCATTCAGCCAACATTCTGCACCGTGACCTCAAACCTTCTAACTTACTGCTC
AACACCACCTGCGATCTCAAGATCTGTGACTTTGGCCTGGCACGTGTTGCAGATCCAGACCATGACCACACAGGCTTCCT
GACAGAATATGTGGCCTCACGCTGGTACAGAGCACCTGAAATCATGCTGAATTCCAAGGGTTACACCAAGTCCATTGACA
TCTGGTCGGTGGGCTGTATTCTGGCTGAGATGTTCTCCAACAGGCCCATTTTCCATGGAAAGCATTACCTTGATCAGCTG
AACCACATTCTCGGCATTCTTGGGTCTCCTTCACAAGAAGACTTGAATCGCATAATAAATCTAAAAGCCAGGATCTATTT
ACTCTCTCTTCCTCACAAAAACAAGGTGCCATGGAATAGACTCTTCCCTCGTGCCGACCCCAAAGCCCTGGACTTATTGG
ATAAGATGTTGATGTTCAACCCTCACAAGAGGATCGAAGTGGAGCAGGCGTTGGCCCACCCCTACCTGGAGCAGTATTAC
GACCCGAGTGACGAGCCTGTGGCCGAAGCCCCATTCAAGTTTGACATGGAGCTGGACAACCTGCCCAAGGGGAAGCTGAA
GGAGCTGATTTTTGAAGAGACTGCTAGATTCCAGCCCGGATACCGATCTTAA

Alignment

ORF - retro_mdom_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 94.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRA
          PRYTNLSYI.EGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTL.EIKILLRFRHENI..INDIIR.
Retrocopy PRYTNLSYIQEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLLEIKILLRFRHENINRINDIIRT

Parental  PAIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCD
          PAIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYF.YQILRGLKYIHSAN.LHRDLKPSNLLLNTTCD
Retrocopy PAIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFPYQILRGLKYIHSANILHRDLKPSNLLLNTTCD

Parental  LKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKH
          LKICDFGLARVADPDHDHTGFLTEYVA.RWYRAPEIMLNSKGYTKSIDIWSVGCILAEM.SNRPIF.GKH
Retrocopy LKICDFGLARVADPDHDHTGFLTEYVASRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMFSNRPIFHGKH

Parental  YLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADPKALDLLDKMLTFNPHKRI
          YLDQLNHILGILGSPSQEDLN.IINLKAR.YLLSLPHKNKVPWNRLFP.ADPKALDLLDKML.FNPHKRI
Retrocopy YLDQLNHILGILGSPSQEDLNRIINLKARIYLLSLPHKNKVPWNRLFPRADPKALDLLDKMLMFNPHKRI

Parental  EVEQALAHPYLEQYYDPSDEPVAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
          EVEQALAHPYLEQYYDPSDEPVAEAPFKFDMELD.LPK.KLKELIFEETARFQPGYRS
Retrocopy EVEQALAHPYLEQYYDPSDEPVAEAPFKFDMELDNLPKGKLKELIFEETARFQPGYRS

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	32.06 RPM	0.00 RPM
SRP007412_cerebellum	8.16 RPM	0.00 RPM
SRP007412_heart	10.37 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	3.02 RPM	0.00 RPM
SRP007412_testis	2.55 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_101 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_101 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010312	1 retrocopy	retro_btau_498,
Ficedula albicollis	ENSFALG00000007935	1 retrocopy	retro_falb_19,
Gallus gallus	ENSGALG00000001501	1 retrocopy	retro_ggal_20,
Myotis lucifugus	ENSMLUG00000005952	1 retrocopy	retro_mluc_302,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101 ,
Ochotona princeps	ENSOPRG00000014484	2 retrocopies	retro_opri_242, retro_opri_615,