RetrogeneDB ID: retro_mdom_1629

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:250032936..250033716(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAS1
• Ensembl ID: ENSMODG00000003252
• Aliases: None
• Description: 2'-5'-oligoadenylate synthetase 1, 40/46kDa [Source:HGNC Symbol;Acc:8086]

Sequence

>retro_mdom_1629
TCATCTGGCAAAGGCACAGCACTGAGAGGACACTCCAAAGCAGACCTGGTGGTATTCCTCAGCAATCTCAAAAGCTATCA
GGACCAGATAGATTGCTGAAATGAGTTCATTGAGGAAATAAAAAAACAGCTGGAAGCATGTCAGCATGAGCAAGGGTGGA
AGTTTGAAGTCAAGTTTGAGGTCTACAGTTCCAGGACCAACCCTCAAGGGCTCAGATTTACTCTGAAGTCAACCAAGATC
CATCAGTGGGTGGACTTTGATGTGCTTCCAGACTTTGATGTTCTAGGCCAACTGACCACAGACTTCAGGAAACCTGACCC
CCAGGTCCACATCATAAAGGAATCCCAGAAAGCAGGAGAATTCTCTACCTGCTTCACAGAACTACAGAAGCAATTCCTCA
GCCAGAGTTGCACCAAGCTCAAAAGTCTGATCCAATTGGTGAAACACTGGTACAAAATGTGCAAGGAGAAAATGGACTCC
CTCCCTCCTCAATATGCTTTTAAGCTCCTGACTGTCTAGGCTTGGAAGCATGAGAGCCAGGAAACTAGATTTATCACAGT
CTGATCCTTTCAGACAGTCCTATACCTGATCCAGAAATACCAAGAATTCATGATCTACTGGACCATCAATTATGACATTG
ATAATGAGATCATTATGGATTATTTCTGTCATCAACTGCGGAAACACAGGCCAGTGATCCTGGACCCAACTGATCCAACT
GGAGATGTGGGAGGTGGAAGTTGATGGCACTGGGGCAAGCCGGCACAAGAAGCTCAAATT

Alignment

ORF - retro_mdom_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 70.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSGKGTALRGLSDADLVVFLSNLQSYQDQIDRRSEFINEIKKQLEACQHEQGWMFEIEFEK-TRFPNPRV
          SSGKGTALRG.S.ADLVVFLSNL.SYQDQID...EFI.EIKKQLEACQHEQGW.FE..FE......NP..
Retrocopy SSGKGTALRGHSKADLVVFLSNLKSYQDQIDC*NEFIEEIKKQLEACQHEQGWKFEVKFEVYSSRTNPQG

Parental  LGFRLKFPGISHSMDFDVLPAFDVLGQLTRDFRKPDPRVYIDLIMESSWNGGEFSTCFTELQKRFLKERV
          L.F.LK...I....DFDVLP.FDVLGQLT.DFRKPDP.V....I...S...GEFSTCFTELQK.FL....
Retrocopy LRFTLKSTKIHQWVDFDVLPDFDVLGQLTTDFRKPDPQVH---IIKESQKAGEFSTCFTELQKQFLSQSC

Parental  TKLKSLIRLVKHWYKMCKKKVDSLPPQYALELLTIYAWEHGSRETSFNTAQGFRTVLYLIQQYQQLLVYW
          TKLKSLI.LVKHWYKMCK.K.DSLPPQYA..LLT..AW.H.S.ET.F.T...F.TVLYLIQ.YQ....YW
Retrocopy TKLKSLIQLVKHWYKMCKEKMDSLPPQYAFKLLTV*AWKHESQETRFITV*SFQTVLYLIQKYQEFMIYW

Parental  TVYYDFEDEIIGNYLRLQLQKCRPVILDPADPTGDVGGGTRWQWGRLAQQARM
          T..YD...EII..Y...QL.K.RPVILDP.DPTGDVGGG..W.WG..AQ.A..
Retrocopy TINYDIDNEIIMDYFCHQLRKHRPVILDPTDPTGDVGGGS*WHWGKPAQEAQI

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_1629 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1629 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
Myotis lucifugus	ENSMLUG00000015764	1 retrocopy	retro_mluc_79,
Monodelphis domestica	ENSMODG00000003252	1 retrocopy	retro_mdom_1629 ,
Mus musculus	ENSMUSG00000032623	1 retrocopy	retro_mmus_2720,