RetrogeneDB ID: retro_mdom_1483

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:255881421..255881785(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S5
• Ensembl ID: ENSMODG00000010026
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 5, muted [Source:HGNC Symbol;Acc:18561]

Sequence

>retro_mdom_1483
GAGAAACAGGGGTTTTGAGAAGTGAGAGGTTCTTGAGAATTCAAAGAATGTGATCCAGGAGACAAATGAACATATCCTTC
CTAAATGTAGAGATGCAGTGCATGACCTCTTGAGTCAGGCTCTCCAGAAATTGCAAGCAGCTACCCATTTAGTCCATAAA
CTTAAGCAAAGGAGCAGGATCAAAGAAAGCTCCATAATCACCACTTATTTATTAGTGAAAAACAGTCCATAACCCAATGG
GAAGATTTCATGAAAGAGCAACACAACAAACAGGGTGCAATGGATGAAAAGCACAAAAAAAGTCACAGAATGCCTTAAAG
AACAATATGCTGAGATGGAGAAAGATCTAGCAAAATTTTCATCT

Alignment

ORF - retro_mdom_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.06 %
• Parental protein coverage: 62.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKRGLREVR-VLENLKNVIQETNEQILPKCRDTMHDHLSQALQKLQAATHLVHKLQQ-KEQEQRKLHNHH
          EK.G..EVR.VLEN.KNVIQETNE.ILPKCRD..HD.LSQALQKLQAATHLVHKL.Q.KEQ.QRKLHNHH
Retrocopy EKQGF*EVR>VLENSKNVIQETNEHILPKCRDAVHDLLSQALQKLQAATHLVHKLKQ<KEQDQRKLHNHH

Parental  LLISEKQRITQWEDFMKEQHSKQSAVDEEHKKA-TERLKEQYAEMEKDLAKFSS
          L.ISEKQ.ITQWEDFMKEQH.KQ.A.DE.HKK..TE.LKEQYAEMEKDLAKFSS
Retrocopy LFISEKQSITQWEDFMKEQHNKQGAMDEKHKKS>TECLKEQYAEMEKDLAKFSS

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_1483 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1483 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699, retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483 ,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179, retro_itri_1901,