RetrogeneDB ID: retro_mdom_362

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:285844000..285844659(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012792
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016129
• Aliases: None
• Description: None

Sequence

>retro_mdom_362
CTGCAGGAAGCGATGTGGCACCAGGCACTGCTGCTCCTGCTTTGGCTGGCCTTTGCTTCAGTGCAGGGTCTTTACTTACA
CATCAGAGAGATGGAGAAGCTCTGCTTCATTGAGGAAATTTCCGACAAGACCATGGTTATCAGGAATTACTGAACTCAGC
TATGGGATAAGCAGACTGAGACCTTTCGGCCCTCCACCCTGGGGCTGGGGATGCATGTATAAGTGAAGGATCCTGAAGGA
AAGGTGGTATTATTGTAGCAGTATGGTTCAGAGGGCCAATTCACGTTTACCTCCCATACCCCAGGTGACCACTAGATCTG
CCTGTACTCTAATTCTACTACAATGACCATCTTTGCGGGAGGCAAACTTAGAGTACATCTGGGTATACAGGTTGGCGAAC
ATACCAACAACTACCCTGAAATTGCTGCCAACGATAAATTAACAGAGCTACAACTTCGTGCCTGCCAGTTGCTTGATCGG
GTGGAACAGATCCAAAAGGAACAGAACTACCAGTGGTATCGTGAAGAACTCTTCCATATGACCTGGAGAGCACAAACCAG
AGAGTGCTGTGGTGGTCCATTGCTCAGACTGTCATCCTTATCCTCACTGGCATCTGGCAGATGAGACACCTCAAGAGTTT
CTTTGAGGCCAACAAGCTT

Alignment

ORF - retro_mdom_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQAAMWRRALLLLLWLAFASVQGLYFHIGETEKRCFIEEIPDETMVIGNYRTQLWDKQTETFLPSTPGLG
          LQ.AMW..ALLLLLWLAFASVQGLY.HI.E.EK.CFIEEI.D.TMVI.NY.TQLWDKQTETF.PST.GLG
Retrocopy LQEAMWHQALLLLLWLAFASVQGLYLHIREMEKLCFIEEISDKTMVIRNY*TQLWDKQTETFRPSTLGLG

Parental  MHVEVKDPEGKVVLSRQYGSEGRFTFTSHTPGDHQICLHSNSTRMTIFAGGKLRVHLDIQVGEHTNNYPE
          MHV.VKDPEGKVVL..QYGSEG.FTFTSHTPGDH.ICL.SNST.MTIFAGGKLRVHL.IQVGEHTNNYPE
Retrocopy MHV*VKDPEGKVVLL*QYGSEGQFTFTSHTPGDH*ICLYSNSTTMTIFAGGKLRVHLGIQVGEHTNNYPE

Parental  IAAKDKLTELQLRARQLLDQVEQIQKEQNYQRYREERFRMT-SESTNQRVLWWSIAQTVILILTGIWQMR
          IAA.DKLTELQLRA.QLLD.VEQIQKEQNYQ.YREE.F.MT..ESTNQRVLWWSIAQTVILILTGIWQMR
Retrocopy IAANDKLTELQLRACQLLDRVEQIQKEQNYQWYREELFHMT<LESTNQRVLWWSIAQTVILILTGIWQMR

Parental  HLKSFFEAKKL
          HLKSFFEA.KL
Retrocopy HLKSFFEANKL

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	245.43 RPM
SRP007412_cerebellum	0.00 RPM	363.34 RPM
SRP007412_heart	0.00 RPM	495.39 RPM
SRP007412_kidney	0.00 RPM	659.73 RPM
SRP007412_liver	0.00 RPM	502.48 RPM
SRP007412_testis	0.20 RPM	274.61 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_362 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_362 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007627	2 retrocopies	retro_eeur_12, retro_eeur_317,
Macropus eugenii	ENSMEUG00000006810	1 retrocopy	retro_meug_1225,
Monodelphis domestica	ENSMODG00000016129	2 retrocopies	retro_mdom_256, retro_mdom_362 ,
Oryctolagus cuniculus	ENSOCUG00000003964	1 retrocopy	retro_ocun_1909,
Ictidomys tridecemlineatus	ENSSTOG00000014658	1 retrocopy	retro_itri_1499,