RetrogeneDB ID: retro_mdom_34

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:484553183..484553618(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023735
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025494
• Aliases: None
• Description: None

Sequence

>retro_mdom_34
ATGGAATTTCCAGACTTGGAAAAGCACTGTTCTGAAGAATCTTGTGGGCAACTAGATTATTTTCCATTAGAATGTGATGG
ATGTAACAAAGCCTTTTGTAAAGATCACCATAAATCCAGTCGCCATAAATGTAGTGATGCCTATAAAAAGGATGTTCAGG
TCCCAGTGTGCCCACTTTGTTGGGCCCCTGTTCCAGTAGGAAGAGGAAAAATTGCAGATATTGTGGTCGGAAAACATATG
GATGGTGATTGTAAATATAACCCAGCTAAGGAAAAACCAAAAATTTTCATACACCGGTGCTCAAAGGAGGGATGTGAGAA
GAAAGAAATGTTCAAGTTGGTGTGTGAACAGTGTCAAGACAACTTCTGTATTAAACACAGACATCCTTTGGCTCATAACT
GCAAACATAGGGATCATCCTATCTCCAAAGCAGGG

Alignment

ORF - retro_mdom_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFPDLGKHCSEKTCKQLDFLPLECDGCNKVFCKDHHKSSRHKCSAAYKKDVQVPVCPLCWAPVPVGRGE
          MEFPDL.KHCSE..C.QLD..PLECDGCNK.FCKDHHKSSRHKCS.AYKKDVQVPVCPLCWAPVPVGRG.
Retrocopy MEFPDLEKHCSEESCGQLDYFPLECDGCNKAFCKDHHKSSRHKCSDAYKKDVQVPVCPLCWAPVPVGRGK

Parental  IADIVVGKHMDDDCKHNPAKEKPKIFIHRCSKEGCKKKEMLKLVCEQCQDNFCIKHRHPLDHNCKHRDHP
          IADIVVGKHMD.DCK.NPAKEKPKIFIHRCSKEGC.KKEM.KLVCEQCQDNFCIKHRHPL.HNCKHRDHP
Retrocopy IADIVVGKHMDGDCKYNPAKEKPKIFIHRCSKEGCEKKEMFKLVCEQCQDNFCIKHRHPLAHNCKHRDHP

Parental  ISKAG
          ISKAG
Retrocopy ISKAG

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_34 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_34 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015776	1 retrocopy	retro_cjac_2957,
Loxodonta africana	ENSLAFG00000005496	1 retrocopy	retro_lafr_211,
Microcebus murinus	ENSMICG00000002112	1 retrocopy	retro_mmur_441,
Monodelphis domestica	ENSMODG00000025494	1 retrocopy	retro_mdom_34 ,
Sarcophilus harrisii	ENSSHAG00000000364	2 retrocopies	retro_shar_756, retro_shar_779,
Tupaia belangeri	ENSTBEG00000007079	2 retrocopies	retro_tbel_2636, retro_tbel_2697,