RetrogeneDB ID: retro_mdom_1357

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:123890098..123891015(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000518
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012785
• Aliases: None
• Description: None

Sequence

>retro_mdom_1357
ATGGCTGACACAGGTGCAAGTGCCAGAGCCGGTGCACAGGAGCAAGATCAGGAAGCAAGTAGGACTCCACCCCTGCAGAC
AGCCAATATGTGGCACAGAGGAGGACCTTCAGGTGGTTGTGAGCTCCTTGCAGATGGAGGCTGGGTTTGAGTGCTGAGAA
AGCATCAGTGGAAACACTAACTGAGAGGTTACAAAGCTACCTTTCAGAAAGTGGGAGGAGGGCTAAGTCCTATTGTGAGC
ACACAGCCAGGACACAGCCAACACTGTCAGATGTTGTGGTGACACTTGTGGAGATGGGTATCGATGTGGAAACTCTCCCT
GCGTGTGCAAAGCAACCCCAGAGGATGGTCATCACAGCACCTCCCGTCACCCGTCGACCTGTGACTCCCAAAGCCCTGAC
TGCTGGGCAGAACAAGTCTCACCCACCTCATATCCCTAGCCATTTCCCTGCATTCCCTGATCCTCAGACCTACATCAAAA
CACCCACATATTGTGAGCTCGTGCCAGACTACCAGGTCCTTCGGGAAAAAGCTGTATCACAGAGGCGAGATGTGGAACGG
GCACTTACCCGTTTTATGGCCAAGACAGGTGAGACACGGAGTCTTTTCAGAGATGGTGTCAGCACATTTCCATTGATTGC
TGCACGACCCTTTACCATTCCCTACCTGACAGCCCTTCTTCCATCTGAATTGGAGATGCGGCAGATGGAAGAGCCTGAGT
CTTGTGAACAGGAAGAACAGACAGACACAGAGAACCTTCCTCTCCACATCAGTAAGGATGAATCAGGTGCTGAGAAAGAG
AATGCCTCAGTTCTACAGCAGAATACTTCCTTGTCAGGAAGCTGGACTAGGGAAGAAGATCTTATTGATAATCCTTATCT
CCGGCCTGCAAAGAAACCCAGGATCCATAGGAAGAAG

Alignment

ORF - retro_mdom_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADTAATAGAGG-SGARSGSKQASTPADNYYLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSYL
          MADT.A.A.AG...GARSGSK..STPAD..Y.A.RRT............G..SAEKASVETLTE.LQSYL
Retrocopy MADTGASARAGA<TGARSGSK*DSTPADSQYVAQRRTFRWL*APCRWRLGL-SAEKASVETLTERLQSYL

Parental  SEIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVETLPAYAKRSQRMVITAPPVTNQPVTPKALTAGQN
          SE.GR.AKSYCEHTARTQPTLSD.VVTLVEMG..VETLPA.AK..QRMVITAPPVT..PVTPKALTAGQN
Retrocopy SESGRRAKSYCEHTARTQPTLSDVVVTLVEMGIDVETLPACAKQPQRMVITAPPVTRRPVTPKALTAGQN

Parental  KSHPPHIPSHFPEFPDPHTYIKTPTYRELVSDYQVLREKAASQRRDVERALTRFMAKTGETQSLFKDDVS
          KSHPPHIPSHFP.FPDP.TYIKTPTY.ELV.DYQVLREKA.SQRRDVERALTRFMAKTGET.SLF.D.VS
Retrocopy KSHPPHIPSHFPAFPDPQTYIKTPTYCELVPDYQVLREKAVSQRRDVERALTRFMAKTGETRSLFRDGVS

Parental  TFPLIAARPFTIPYLTALLPSELEMQQMEETDSSEQDEQTDTENLPLHISTDESGAEKENASVLQQNTSL
          TFPLIAARPFTIPYLTALLPSELEM.QMEE..S.EQ.EQTDTENLPLHIS.DESGAEKENASVLQQNTSL
Retrocopy TFPLIAARPFTIPYLTALLPSELEMRQMEEPESCEQEEQTDTENLPLHISKDESGAEKENASVLQQNTSL

Parental  SGSRTGEENLIDNPYLRPVKKPKIRRKK
          SGS.T.EE.LIDNPYLRP.KKP.I.RKK
Retrocopy SGSWTREEDLIDNPYLRPAKKPRIHRKK

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_1357 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1357 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357 ,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,