RetrogeneDB ID: retro_mdom_82

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:521526471..521527986(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023150
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012925
• Aliases: None
• Description: None

Sequence

>retro_mdom_82
ATGGTGTTAGCAGATCTTGGAAGAAAAATAACCTCAGCACTACGCTCATTGAGCAATGCCACCATTATCAATGAAGAGGT
TTTAAATGCTATGCTAAAAGAAGTATGCACAGCCTTATTGGAAGCAGATGTTAATATTAAGCTGGTGAAGCAGCTCCGAG
AAAATGTCAAGTCTGCAATTGATCTTGAAGAAATGGCATCAGGTCTAAACAAAAGAAAAATGATTCAGCATGCTGTATTT
AAGGAACTTGTGAAGCTTGTAGACCCTGGAGTTAAAGCCTGGACACCAACCAAAGGGAAACCAAATGTTATTATGTTTGT
TGGGTTGCAGGGTAGTGGTAAAACCACAACATGTTCTAAGTTAGCGTATTATTACCAGAGAAAAGGTTGGAAGACTTGTT
TGATATGTGCAGACACATTCAGAGCAGGAGCTTTTGACCAGCTAAAACAGAATGCTACAAAAGCAAGAATTCCATTCTAT
GGAAGCTATACAGAAATGGACCCTGTGATCATTGCCTCTGAAGGTGTGGAAAAATTCAAAAATGAAAACTTTGAAATTAT
TATTGTTGATACAAGCGGCCGTCATAAACAAGAAGATTCTTTGTTTGAAGAAATGCTCCAAGTAGCTAATGCTATACAAC
CTGACAACATCGTTTATGTAATGGATGCTTCCATCGGTCAGGCTTGTGAAGCACAAGCTAAGGCTTTCAAAGACAAAGTA
GATGTAGCCTCGGTAATTGTGACAAAACTTGATGGCCATGCAAAAGGTGGTGGTGCACTTAGTGCTGTTGCTGCCACCAA
AAGTCCTATAATTTTCATTGGTACTGGCGAGCATATAGATGACTTTGAACCTTTTAAAACACAGCCTTTCATCAGCAAAC
TTCTTGGTATGGGCGATATTGAAGGATTGATAGATAAAGTCAATGAATTAAAGTTGGATGACAATGAAGCACTTATAGAA
AAGCTGAAACATGGTCAGTTTACATTGAGAGATATGTATGAACAATTCCAAAACATCATGAAAATGGGCCCGTTCAGTCA
AATATTGGGTATGATCCCTGGTTTTGGAACAGATTTTATGAGCAAAGGCAACGAACAAGAGTCAATGGCAAGGCTAAAAA
AACTGATGACAATAATGGACAGTATGAATGATCAAGAACTTGACAGTACAGATGGTGCAAAAGTTTTCAGTAAACAACCA
GGAAGAATCCAAAGAGTAGCAAGAGGATCAGGTGTCTCAACAAGAGATGTTCAGGAGCTTTTGACACAATATACAAAGTT
TGCTCAAATGGTAAAAAAGATGGGTGGTATCAAAGGACTTTTCAAAGGAGGTGACATGTCAAAGAATGTAAGCCAATCCC
AGATGGCAAAACTAAACCAACAAATGGCCAAAATGATGGATCCAAGAGTACTTCATCATATGGGAGGTATGGCAGGACTA
CAGTCAATGATGAGGCAGTTTCAACAAGGAGCTGCTGGAAATATGAAAGGCATGATGGGATTCAATAATATGTGA

Alignment

ORF - retro_mdom_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDLEEMASGLN
          MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDLEEMASGLN
Retrocopy MVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRENVKSAIDLEEMASGLN

Parental  KRKMIQHAVFKELVKLVDPGVKAWTPTKGKPNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTF
          KRKMIQHAVFKELVKLVDPGVKAWTPTKGKPNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTF
Retrocopy KRKMIQHAVFKELVKLVDPGVKAWTPTKGKPNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTF

Parental  RAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVAN
          RAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVAN
Retrocopy RAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVAN

Parental  AIQPDNIVYVMDASIGQACEAQAKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHID
          AIQPDNIVYVMDASIGQACEAQAKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHID
Retrocopy AIQPDNIVYVMDASIGQACEAQAKAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHID

Parental  DFEPFKTQPFISKLLGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILG
          DFEPFKTQPFISKLLGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILG
Retrocopy DFEPFKTQPFISKLLGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILG

Parental  MIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL
          MIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL
Retrocopy MIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQEL

Parental  LTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQG
          LTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQG
Retrocopy LTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQG

Parental  AAGNMKGMMGFNNM
          AAGNMKGMMGFNNM
Retrocopy AAGNMKGMMGFNNM

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	38.02 RPM
SRP007412_cerebellum	0.00 RPM	30.03 RPM
SRP007412_heart	0.00 RPM	24.12 RPM
SRP007412_kidney	0.00 RPM	32.92 RPM
SRP007412_liver	0.00 RPM	40.28 RPM
SRP007412_testis	0.00 RPM	53.82 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_82 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_82 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012925	1 retrocopy	retro_mdom_82 ,
Tupaia belangeri	ENSTBEG00000011409	1 retrocopy	retro_tbel_4420,