RetrogeneDB ID: retro_mdom_1314

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:412492659..412493077(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED22
• Ensembl ID: ENSMODG00000012748
• Aliases: None
• Description: mediator complex subunit 22 [Source:HGNC Symbol;Acc:11477]

Sequence

>retro_mdom_1314
ATGGCCCAACAAAGAGTTCTCCCCCCAGAGCAAAGAGACCCTCCTTCAGTCCTACAATAAGAGGCTGAAAGATGACGTTA
AGTGGATTATGGATAATTTCACTTAGATCATAAAGACAGCAAAGATTGAAAATGAAACTCAGGTCTCCCGGGCAACTCAG
GGAGAGCAGGACAATTATGAGATGCATGTGAGAGCTGCCAATATTGTCCATGCTGGGGAATCTCCGATGAAGCTTGTGTC
TGACCTCAAGCAATTTCTCATCCTCAATGACTTTCCCTCGATGAATGAAGCCATTGATCAGAGTAACCAGCAGCTTCAAA
GCTTGCAGGATGAATGTGACAAGAAGCTCATTTCCCTGCAGGATGAGATATCCATTGACTTATATGAGCTAGAGGAGGAG
TATTACTCGTCCAGGTAC

Alignment

ORF - retro_mdom_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 68.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQQRVLP-QSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYEMHVRAANIV
          MAQQRVLP.QSKETLLQSYNKRLKDD.K.IMDNFT.IIKTAKIE.ETQVSRATQGEQDNYEMHVRAANIV
Retrocopy MAQQRVLP>QSKETLLQSYNKRLKDDVKWIMDNFT*IIKTAKIENETQVSRATQGEQDNYEMHVRAANIV

Parental  RAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRSLQDECDKKLISLRDEISIDLYELEEEYYSSSY
          .AGES.MKLVSDLKQFLILNDFPS.NEAIDQ.NQQL.SLQDECDKKLISL.DEISIDLYELEEEYYSS.Y
Retrocopy HAGESPMKLVSDLKQFLILNDFPSMNEAIDQSNQQLQSLQDECDKKLISLQDEISIDLYELEEEYYSSRY

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	41.84 RPM
SRP007412_cerebellum	0.00 RPM	59.74 RPM
SRP007412_heart	0.00 RPM	68.98 RPM
SRP007412_kidney	0.00 RPM	121.15 RPM
SRP007412_liver	0.00 RPM	86.10 RPM
SRP007412_testis	0.00 RPM	54.41 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1314 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1314 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004674	1 retrocopy	retro_mluc_96,
Monodelphis domestica	ENSMODG00000012748	1 retrocopy	retro_mdom_1314 ,