RetrogeneDB ID: retro_mdom_1047

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:374333258..374333635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD7
• Ensembl ID: ENSMODG00000019450
• Aliases: None
• Description: COMM domain containing 7 [Source:HGNC Symbol;Acc:16223]

Sequence

>retro_mdom_1047
GAATATGCAGCCAAGACTGAAGTGCGTTTTCCCTTTGTAGTGAAATCCAAGGAAGGTGAAATATTTATTTGAGTAACTTA
GCTCACTTTGCTGCCTACAATCAGATTAAACTAAAGTTCTTGAGAATATTGGGAAAAAGCCTTCTTCTAGTCCCTAACTG
TGTCTTAAAGAAAATAAGACTGTGGACCTGGTCAGAATAGCTAGCTTTTATTATTCTGGACCTAGTGAACAGAAAACCAC
TTATTTTTCTGAAGAGTGGAAAACATATTTTTCCCATCCTTTCCAGATGGGCAGTAGGACAGCTGATAATGATTCACCAA
CTTATAGACATAGAATGGAAATTTGGAGTGATGTATGGGAGCAGCCAACTGCAAAAG

Alignment

ORF - retro_mdom_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.81 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QFAALTEVIFYFLVQ-PKEVE-TFLAKLSDFAVTNQISLGPLKNIVKSLLLVPNGALKK-NMTAEQVR-A
          ..AA.TEV.F.F.V..P..V....L..L..FA..NQI.L..L....KSLLLVPN..LKK.N.T...VR.A
Retrocopy EYAAKTEVRFPFVVK>PRKVK>IYLSNLAHFAAYNQIKLKFLRILGKSLLLVPNCVLKK<NKTVDLVRIA

Parental  DFITLGLGEEKATYFSEKWKQKS-PILARWAIGQTLMINQLIDMEWKFGVTSGSSELQK
          .F...G..E.K.TYFSE.WK....PIL.RWA.GQ..MI.QLID.EWKFGV..GSS.LQK
Retrocopy SFYYSGPSEQKTTYFSEEWKTYF>PILSRWAVGQLIMIHQLIDIEWKFGVMYGSSQLQK

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	131.71 RPM
SRP007412_cerebellum	0.00 RPM	164.53 RPM
SRP007412_heart	0.00 RPM	100.47 RPM
SRP007412_kidney	0.00 RPM	176.46 RPM
SRP007412_liver	0.00 RPM	126.88 RPM
SRP007412_testis	0.00 RPM	64.23 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1047 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1047 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008561	2 retrocopies	retro_chof_1254, retro_chof_345,
Loxodonta africana	ENSLAFG00000008789	1 retrocopy	retro_lafr_1194,
Macropus eugenii	ENSMEUG00000010627	1 retrocopy	retro_meug_1062,
Monodelphis domestica	ENSMODG00000019450	3 retrocopies	retro_mdom_1047 , retro_mdom_313, retro_mdom_890,
Sarcophilus harrisii	ENSSHAG00000006762	1 retrocopy	retro_shar_142,
Ictidomys tridecemlineatus	ENSSTOG00000006640	1 retrocopy	retro_itri_311,