RetrogeneDB ID: retro_mdom_1507

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:54159800..54160292(-)
• Located in intron of: ENSMODG00000020745

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012129
• Aliases: None
• Description: None

Sequence

>retro_mdom_1507
GTGAGGCCAGTTCATGGGTTAATTTTTCTTTTCAAGTGGCAGCTTGAAGAACCAGGAGGTTCTGTTGTTCAGGATTCCAG
ACTTGACACAATTTTTTTTGCAAAACAGGTAATAAATAATGCTTGTGCACCTCAGGCCATAGTCAGTGTACTATTGAATT
GTACCCATCAAGATGTCCATCTAGGGGAGATGCTTTCAGAACATGAAGAATTTTCACAATCGTTTTGATGCTACAATGAA
AGGCTTGGCAGCAAGTAAATCAGAAGTGATCCGACAAGTTCACAACAGTTTTGCCAGTCAACAGATGTTTGAATTTGATG
CAAAAACATTAGCAAAAGAAGATGCTTTTCATTTTGTTATGTTCCTGTCAATAGAAGGCTATATGAATTAGATGGATTAA
GAGAAGGACCAAATGATTTAAGCATTTAGGTATGTAATCAATTAGATTGGATTAGTGCAGTAAGACCAGTTATAGAGAAA
AGAATACAAAAA

Alignment

ORF - retro_mdom_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.07 %
• Parental protein coverage: 76.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFK
          ..PVHGLIFLFKWQ..EEP.GSVVQDSRLDT...AKQVINNACA.QAIVSVLLNCTHQDVHLGE.LSE..
Retrocopy VRPVHGLIFLFKWQL-EEPGGSVVQDSRLDTXXXAKQVINNACAPQAIVSVLLNCTHQDVHLGEMLSEHE

Parental  EFSQSF-DAAMKGLALSNSEVIRQVHNSFARQQMFEFDAKTSAKEEDA-FHFVSYVPVSGRLYELDGLRE
          EFSQSF.DA.MKGLA.S.SEVIRQVHNSFA.QQMFEFDAKT.AK.EDA.F.F..YVPV..RLYELDGLRE
Retrocopy EFSQSF>DATMKGLAASKSEVIRQVHNSFASQQMFEFDAKTLAK-EDA<FSFC-YVPVNRRLYELDGLRE

Parental  GPIDLG--ACNQEDWINAVRPVIEKRIQK
          GP.DL....CNQ.DWI.AVRPVIEKRIQK
Retrocopy GPNDLSI*VCNQLDWISAVRPVIEKRIQK

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_1507 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1507 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015914	1 retrocopy	retro_amel_1462,
Monodelphis domestica	ENSMODG00000012129	1 retrocopy	retro_mdom_1507 ,
Mustela putorius furo	ENSMPUG00000004619	1 retrocopy	retro_mputfur_259,
Ictidomys tridecemlineatus	ENSSTOG00000000772	1 retrocopy	retro_itri_1814,