RetrogeneDB ID: retro_mdom_79

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:56229901..56230453(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017902
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:F6U8T8]

Sequence

>retro_mdom_79
ATGGAGTACCTTATCGGCATCCAAGGGTCTGACTACATTTTGGTGGCCTCCGACTGCGTGGCCGCCAGCAACATTGTCCA
GATGAGTGTAGGAGAGGCTGGAGACACTGTTCAGTTTGCTGAATACATTCAGAAAAACGTACAGCTCTACAAGATGCGCA
ATGGGTATGAATTGTCCCCCACAGCAGCAGCTAACTTCACACACCGCAATCTGGCTTACTACCTCCGGACTCGGACCCCA
TACCACGTCAACCTCCTTTTGGCTACCTATGATGAACATGAAGGCCCTGCACTGTACTACATGGGTTACCTGGCAGCACT
GGCCAAAGCTCCATTTGCAGCCCATGGTTATGGTGCCTTTTTGACCCTCAGCATCCTAGATCATTTTTATAAACCAAGTA
TCACACGTGAGGAGGCAGTAGAACTCCTGAAGAAATGTCTGGAAGAGCTCCAGAAGCGCTTCATCTTGAACTTGCCTTCC
TTCAGCGTCCGGATCATCGACAAAGATGGAATCCATGACCTGGACATCATCGTCCCTTCAAAGAAGTCCTAA

Alignment

ORF - retro_mdom_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 80.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGRYFSPERASCLPGEARAGPLKPLTPYHVNLLLAGYD
          ...I....VGEAGDTVQFAEYIQKNVQLYKMRNG...SP..A........A..L...TPYHVNLLLA.YD
Retrocopy ASNIVQMSVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTHRNLAYYLRTRTPYHVNLLLATYD

Parental  EHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYKPSITREEAVELLKKCLEELQKRFILNLPSF
          EHEGPALYYM.YLAALAKAPFAAHGYGAFLTLSILD..YKPSITREEAVELLKKCLEELQKRFILNLPSF
Retrocopy EHEGPALYYMGYLAALAKAPFAAHGYGAFLTLSILDHFYKPSITREEAVELLKKCLEELQKRFILNLPSF

Parental  SVRIIDKDGIHDLDTIVPSKKS
          SVRIIDKDGIHDLD.IVPSKKS
Retrocopy SVRIIDKDGIHDLDIIVPSKKS

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_79 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_79 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79 ,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,