RetrogeneDB ID: retro_mdom_1915

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:112888952..112889404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024791
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSMODG00000023728
• Aliases: None
• Description: general transcription factor IIH, polypeptide 3, 34kDa [Source:HGNC Symbol;Acc:4657]

Sequence

>retro_mdom_1915
ATGAAATCAAGAATATTGGTCATTAAGGCTGCAGAAGACAGTGCATTACAATATATGAACCTCATGAATGTTATTTTTGG
AGCACAGAAACAGAATATCGTGATTGATGCTTGTGTCCTAGATGCAGATTCAGGGCTCCTCCAACACGCCTGGGACATTA
CCAGGGGCATATACTTGAAGGTGCCCCAGATGTCATCTCTTCTGCAGTATTTATTATGGGTATTTCTTCCTGATCAAGAC
CAAAGGTCTCAGTTAAACCTCCCACCGCCAATTCATGTTGACTACAGAGCTGCTGCTTCTGCCATAGAAATCTCATTGAA
ATTGGATACGTCTGCTCTGTATGTTTGTCAATATTCTGCAATTTCAGCCCTATTTGTACCACATGCAAGACAGCCTTCAA
GATTTCTCTGCCTCCTGTTCTGAAAGCCAAGAAGAAGAAATGAAAAGCTTCT

Alignment

ORF - retro_mdom_1915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSRILVIKAAEDSALQYMNFMNVIFAAQKQNIVIDACVLDADSGLLQQACDITGGIYLKVPQMPSLLQY
          MKSRILVIKAAEDSALQYMN.MNVIF.AQKQNIVIDACVLDADSGLLQ.A.DIT.GIYLKVPQM.SLLQY
Retrocopy MKSRILVIKAAEDSALQYMNLMNVIFGAQKQNIVIDACVLDADSGLLQHAWDITRGIYLKVPQMSSLLQY

Parental  LLWVFLPDQDQRSQLNLPPPIHVDYRAA-CFCHRNLIEIGYVCSVCLSIFCNFSPICTTCETAFKISLPP
          LLWVFLPDQDQRSQLNLPPPIHVDYRAA.CFCHRNLIEIGYVCSVCLSIFCNFSPICTTC.TAFKISLPP
Retrocopy LLWVFLPDQDQRSQLNLPPPIHVDYRAA<CFCHRNLIEIGYVCSVCLSIFCNFSPICTTCKTAFKISLPP

Parental  VLKAKKKKLKAS
          VLKAKKKK.KAS
Retrocopy VLKAKKKK*KAS

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_1915 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1915 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915 ,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550, retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357,