RetrogeneDB ID: retro_mdom_593

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:436667192..436667920(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014491
• Aliases: None
• Description: None

Sequence

>retro_mdom_593
TCTAACCTGTTTCTCACCTGGAGTGAATGTCAGGCACAAGTGAACTGATTTCCTGCTGCCATGTTCAAGAAGTTTGCTAC
TGAGGATGAGACTTGGGCCTTTGTTTGATAAACTACAAGCCCTGGTCATTCTATAGAATCAAAAAATAAATGTAACATAC
AAGACCCCCAAATGAAGCCAATAAAGAGACCGCCAGGAGTCCTCAAATGAAGAGGAATAACCTAGCCCCAAACTTGCAAG
ACAAAATACAGACTCATTACCTTCACTTAGCAGATTTATTTTCTTTTATGGGAAATGCCACTGTAATTTACACAAATGGC
TGCTGCTCCAGTAATGAAATAAGGAAAGCCTGAGCAGTCATTGAAGTTTATTGGGGGCCAGGCTATCCCCTAAATGTGGG
TGATAGACTTCCTGGGTGACAGACAAACCAAAGAGCAGAACTACATGGTACCTTCAAAGCAAATGAATAAGCAAAGAATC
AAAACATCAGTGAGCTGGTTATCTACACAGTTAGCAGGTTTATTCAAAATTGGGTTAAAAGCTGGAAGAAAAATGTCTGG
AAAATAAGCCCAGGAAATGATGTCATCAACAAAGAAGACTATGTGAAGCTCCATGTACTTACTCAAGGAACAGACATTAA
ATGGGTATGTGTTTCTGGTCATTTGAGGTTTGTAGGAAATAAAGAAGCTGATAGATTACCAAAGGAAGGAGCTAAAAAAT
CTCAAGAC

Alignment

ORF - retro_mdom_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.27 %
• Parental protein coverage: 86.36 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGVFLTWSECQAQVNRFPAARFKKFATEDEAWAFVRNATSPDRSTEQKKKCGTQD-PKFKPNKRPRESSD
          ...FLTWSECQAQVN.FPAA.FKKFATEDE.WAFV...TSP..S.E.K.KC..QD.P....NK....S..
Retrocopy SNLFLTWSECQAQVN*FPAAMFKKFATEDETWAFV**TTSPGHSIESKNKCNIQD<PPNEANKETARSPQ

Parental  EDEEPCSKLAKQAMDTVPSLSKDIFSYMGDAAVVYTDGCCSSNGRRKARAGIGVYWGPGHPLNVADRLLG
          ...............T......D.FS.MG.A.V.YT.GCCSSN..RKA.A.I.VYWGPG.PLNV.DRL.G
Retrocopy MKRNNLAPNLQDKIQTHYLHLADLFSFMGNATVIYTNGCCSSNEIRKA*AVIEVYWGPGYPLNVGDRLPG

Parental  RQTNQRAEIHAACKAIEQAKNQNINKLVLYTDSMFTINGITSWIKDWKKNGWKTSTGKEVINKEDFVKLD
          .QTNQRAE.H...KA.E.AKNQNI..LV.YT.S.F....I..W.K.WKKN.WK.S.G..VINKED.VKL.
Retrocopy *QTNQRAELHGTFKANE*AKNQNISELVIYTVSRF----IQNWVKSWKKNVWKISPGNDVINKEDYVKLH

Parental  TLTQGIDIKWIHVPGHSGFAGNEEADRLAREGAKKSQE
          .LTQG.DIKW..V.GH..F.GN.EADRL..EGAKKSQ.
Retrocopy VLTQGTDIKWVCVSGHLRFVGNKEADRLPKEGAKKSQD

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	34.81 RPM
SRP007412_cerebellum	0.00 RPM	34.28 RPM
SRP007412_heart	0.00 RPM	45.85 RPM
SRP007412_kidney	0.00 RPM	22.39 RPM
SRP007412_liver	0.00 RPM	32.73 RPM
SRP007412_testis	0.20 RPM	60.89 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_593 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_593 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593 ,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,