RetrogeneDB ID: retro_mdom_166

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:266725098..266726127(-)
• Located in intron of: ENSMODG00000011021

Retrocopy information

• Ensembl ID: ENSMODG00000024043
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016902
• Aliases: None
• Description: None

Sequence

>retro_mdom_166
ATGGAGAAACTTAAAGCAGAGATCGGTCAGAAGCGCAAGCTGGTGGAGGACCAGAATCTGCTTGGGGAAAGGAAAAAATA
CTTTAAACGTAGTGACCTTGCCAAAAAAGAAGAGGAGGCCTACTTTGAAAGATCTGGCTACAAGGTACAGCCAAAAGAGA
AGGATCAGAAACCATTACCTTCACCCAATCCAGTATTAGAAGTGGAACCAGCAGAGGGAAAATCGCCTGTGACTCTTTCA
AGGCCACAGGTCCTCAGGCAGTTCAGAGAAAGAGGAGAACCAGTGAGATTGTTTGGAGAAACTGACTATGACGCATTTCT
ACGTTTAAGAAAGATAGAGATTCTCACACCAGAGGTTAACAGGGGTTTAAGGAACGACTTGAAGGCAGCTTTGGATAAGA
TCGATCAACAGGACCTTGATGAAATGGCTAGTGGTCAAGAACCAGGAGAAAATGACACACAGAATGACCTGAAAGTCCAT
GAAGAAAATACCACTTTTGAAGAATTAGAGGCTTTGGGAAAATCCTTAGGAAAGGGGGATGATCAAGAAGACATGGACAT
CATAACCAAAGTCCTTAAGTTTCTCCTTGGAGTTTGGGCTAAGGAACTCAATGCTAGAGAAGACCATGTAAAACAAAGCG
TTCAGGGCAAACTGAACAGTGCCACCCACAAACAGACAGAAGCCTATCTGAGGCCACTCTTCAGAAAGCTACAGAAAAGG
ACTCTTCCTGCAGATATCAAAGAATCAATAACAAACATTATCAAGTTCTTGCTGCAGAGAGAATATGTGAAGGCAAACGA
TGCTTATCTTCAGATGGCCATTGGAAGTGCTCCCTGGCCAATTGGAGTCACCATGGTTGGTATCCATGCCAGAACCGGTC
GGGAAAAGATTTTTTCCAAGCATGTTGCACATGTTCTAAATGATGAGACTCAAAGAAAATATATTCAGGGTCTGAAAAGA
TTAATGACCATTTGTCAGAAGCACTTCTCAACAGACCCCTCAAAGTGTGTGGAGTACAATGCCCTCTGA

Alignment

ORF - retro_mdom_166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 87.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRQLVEDKKLLGESKRYFKRSELAKKEEEAYFERCGYKPVNEKPTGEVQPKEEDQKPLASSNPVLELELA
          K.......KL.........R....K....A..E...Y....E.....VQPKE.DQKPL.S.NPVLE.E.A
Retrocopy KAEIGQKRKLVEDQNLLGERKKYFKRSDLAKKEEEAYF---ERSGYKVQPKEKDQKPLPSPNPVLEVEPA

Parental  EEKLPMTLSRQEVIRRLRERGEPVRLFGETDYDAFQRLRKIEILTPEVNKGLRNDLKAALDKIDQQYLNE
          E.K.P.TLSR..V.R..RERGEPVRLFGETDYDAF.RLRKIEILTPEVN.GLRNDLKAALDKIDQQ.L.E
Retrocopy EGKSPVTLSRPQVLRQFRERGEPVRLFGETDYDAFLRLRKIEILTPEVNRGLRNDLKAALDKIDQQDLDE

Parental  IVGGQEPGEEDTQNDLKVHEENTTIEELEALGESLGKGDDHKDMDIITKFLKFLLGVWAKELNAREDYVK
          ...GQEPGE.DTQNDLKVHEENTT.EELEALG.SLGKGDD..DMDIITK.LKFLLGVWAKELNARED.VK
Retrocopy MASGQEPGENDTQNDLKVHEENTTFEELEALGKSLGKGDDQEDMDIITKVLKFLLGVWAKELNAREDHVK

Parental  RSVQGKLNSATQKQTESYLRPLFRKLRKRTLPADIKESITDIIKFMLQREYVKANDAYLQMAIGNAPWPI
          .SVQGKLNSAT.KQTE.YLRPLFRKL.KRTLPADIKESIT.IIKF.LQREYVKANDAYLQMAIG.APWPI
Retrocopy QSVQGKLNSATHKQTEAYLRPLFRKLQKRTLPADIKESITNIIKFLLQREYVKANDAYLQMAIGSAPWPI

Parental  GVTMVGIHARTGREKIFSKHVAHVLNDETQRKYIQ
          GVTMVGIHARTGREKIFSKHVAHVLNDETQRKYIQ
Retrocopy GVTMVGIHARTGREKIFSKHVAHVLNDETQRKYIQ

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_166 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_166 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	ENSMODG00000016902	1 retrocopy	retro_mdom_166 ,
Otolemur garnettii	ENSOGAG00000007294	1 retrocopy	retro_ogar_1279,
Sarcophilus harrisii	ENSSHAG00000016463	1 retrocopy	retro_shar_77,