RetrogeneDB ID: retro_mdom_640

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:643331972..643332710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCMTD1
• Ensembl ID: ENSMODG00000009645
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 [Source:HGNC Symbol;Acc:30483]

Sequence

>retro_mdom_640
GAACTTCACTCAGATGTGGTGGAATATGCCAAGGAAAAACTCGAGATCTTCATCAAAAATAGTGATAGTTATGACAAATT
TGAGTTCTCTGAACCAGCATTTGTGGCAGGTAACTGCCTAGAGATAGCATCCGATAGCCATCAGTATGACCGGATTTATT
GTGGAGCTGGTGTCCAGAAAGACCATGAAAACTACATGAAAATATTATTGAAAGTGGGAGGTATTCTAGTCATGCCTATA
GAAGATCAGTTAACTCAAATTATGCAAACTGGACAGAATACTTGGGAAAGGAAAAGCATCCTTGCTGTTTCTTTCACTCC
ATTAATACAACCAAATAGAAATGACAATAGCAAACCAGATTCAGTGGGATTACCTCCTTGTGCTGTCAGGAATCTTCAAG
GCTTGGTTTGGATTTATATTCTACATACACTTAGAAACTTCATAAATGATGAGATGCAAGCCAAGGGTATTTCTCAGAGG
GCTCCTCCCAAAAGAAAAAGGAAGAGCGTTAAACAAAGAATCAATGCATATGTGTTTGTAGGCAATCAACTTATTCCTCA
GCCTCTAGACAGTGAGGATGATGAAAAAATGGAAGAAGACCACAAAGAAGAGGAAGAGAAAGACCAGGGTGAAACCTTGA
AGCCAGAGGAACCCCCTCAGAATCTATTGAGAGGGAAAATCATGTGAATACCCCTGCCAGAGTCTTTAAAAGTGTATTTG
ACCTATTTTAGAGATAAA

Alignment

ORF - retro_mdom_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 68.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELHSDVVEYAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL
          ELHSDVVEYAKEKLE.FIKNSDS.DKFEF.EPAFV.GNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL
Retrocopy ELHSDVVEYAKEKLEIFIKNSDSYDKFEFSEPAFVAGNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL

Parental  KVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLIQPNRNDNSKPDSVGLPPCAVRNLQDLARIYI
          KVGGILVMPIEDQLTQIM.TGQNTWE.K.ILAVSF.PLIQPNRNDNSKPDSVGLPPCAVRNLQ.L..IYI
Retrocopy KVGGILVMPIEDQLTQIMQTGQNTWERKSILAVSFTPLIQPNRNDNSKPDSVGLPPCAVRNLQGLVWIYI

Parental  RRTLRNFINDEMQAKGISQRAPPKRKRKRVKQRINTYVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG
          ..TLRNFINDEMQAKGISQRAPPKRKRK.VKQRIN.YVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG
Retrocopy LHTLRNFINDEMQAKGISQRAPPKRKRKSVKQRINAYVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG

Parental  ETLKPEEPPQNLLREKIMRLPLPESLKAYLTYFRDK
          ETLKPEEPPQNLLR.KIM..PLPESLK.YLTYFRDK
Retrocopy ETLKPEEPPQNLLRGKIM*IPLPESLKVYLTYFRDK

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_640 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_640 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
Cavia porcellus	ENSCPOG00000006593	1 retrocopy	retro_cpor_63,
Monodelphis domestica	ENSMODG00000009645	1 retrocopy	retro_mdom_640 ,
Oryctolagus cuniculus	ENSOCUG00000016958	2 retrocopies	retro_ocun_1571, retro_ocun_1682,