RetrogeneDB ID: retro_mdom_1055

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:424139108..424139879(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSMODG00000004283
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_mdom_1055
ATGGGCCGGGTGATTTGTGGTCAGAGGAAGGGAGCGGGCTCCATCTTCTGAGCTCGTGTGAAGCACCAAAAAGGGGCAGC
GAAGCTGCGGGCCGTAGACTTCACTGAGAAGCATGGTTACATCAAGGGTATTGTAAAGGACATAATCCATGATCCAGGTT
GAGGGGCTCCTCTTGCAAAAGTAGCTTTCAGAGATCCATACCGATTTAAAAAGAGGACAGAGTTGTTCATTGCTGCTGAA
GGCATTTACACTGGCCAGTTTGTAGACTGTGGTAAGAAAGCTACACTCAACACTGGCAATGTCCTCCCAGTTGGCACTGT
GCCTGAAGGAACTATTGTGTGCTGTCTTGAAGAAAAGCCTGGTGACAGGGGTAAGCTTGCCCGTGCATCTGGAAACTATG
GCACAGTTATTTCACACAATCCCGAAACCAAGAAAACACGGGTGAAGCTACCTTCAGGCTCTAAGAAAGTGATCTCCTCT
GCAAACAGAGCCATAGTTGGTATTGTTGCTGGTGGAAGTCATATTGATAAATCCATCCTTAAGGCAGGTCGTGCCTACCA
CAAATATAAGGCCAAGAGAAACTGCTGGCCTCAAGTCCAGGGTGTGGCCATGCATCCTGTGGAACATCCCTTTGGAGGAG
GTAATCACCATCATATTGGAAAACCATCCACCATTTGAAGAGATGCCTCAGCTGGACGAAAGGTTGGTCTCATTGCTGCC
TGGCATACTGGTTGACTCCGGGGTACCAAGACTGTACAGGAGAAGGAGAAC

Alignment

ORF - retro_mdom_1055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRVIRGQRKGAGSVFRAHVKHRKGAAKLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVAFRDPYRFK
          MGRVI.GQRKGAGS.F.A.VKH.KGAAKLRAVDF.E.HGYIKGIVKDIIHDPG.GAPLAKVAFRDPYRFK
Retrocopy MGRVICGQRKGAGSIF*ARVKHQKGAAKLRAVDFTEKHGYIKGIVKDIIHDPG*GAPLAKVAFRDPYRFK

Parental  KRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
          KRTELFIAAEGI.TGQFV.CGKKA.LN.GNVLPVGT.PEGTIVCCLEEKPGDRGKLARASGNY.TVISHN
Retrocopy KRTELFIAAEGIYTGQFVDCGKKATLNTGNVLPVGTVPEGTIVCCLEEKPGDRGKLARASGNYGTVISHN

Parental  PETKKTRVKLPSGSKKVISSANRAIVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
          PETKKTRVKLPSGSKKVISSANRAIVG.VAGG..IDK.ILKAGRAYHKYKAKRNCWP.V.GVAM.PVEHP
Retrocopy PETKKTRVKLPSGSKKVISSANRAIVGIVAGGSHIDKSILKAGRAYHKYKAKRNCWPQVQGVAMHPVEHP

Parental  FGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
          FGGGNH.HIGKPSTI.RDA.AGRKVGLIAA..TG.LRGTKTVQEKEN
Retrocopy FGGGNHHHIGKPSTI*RDASAGRKVGLIAAWHTG*LRGTKTVQEKEN

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_1055 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1055 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 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Macropus eugenii	ENSMEUG00000013824	9 retrocopies	retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica	ENSMODG00000004283	3 retrocopies	retro_mdom_1055 , retro_mdom_1696, retro_mdom_253,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Ornithorhynchus anatinus	ENSOANG00000002646	1 retrocopy	retro_oana_93,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Sarcophilus harrisii	ENSSHAG00000013568	2 retrocopies	retro_shar_482, retro_shar_558,