RetrogeneDB ID: retro_mdom_1114

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:144668534..144671312(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005755
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRPF4B
• Ensembl ID: ENSMODG00000009756
• Aliases: None
• Description: PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Source:HGNC Symbol;Acc:17346]

Sequence

>retro_mdom_1114
GAGTTTATTGATGCCTCTGACAAAGATGGGGCATCTCCACCAAAAAGAACTAAAATTGATGACTTAGCTTTGCTGGAAGA
TTTGGAGAAACAGAGAGCTTTAATTAAAGCTGAACTTGATAATGAGTTGATGGAAGGAAAAGTCCAGTCTGGAATGGGGC
TAATATTACAGGGTTATGATTCAGGATCCGAAGAAGAGGGAGAAATACATGAGAAGGTGAGAAATGGGAATAGATCAACT
GCTAGGTCATCAAATACTAAGGCAAAACTTGAACTCGTAGACAATAAAAAGCATTCAAAGAAATGAAGCAAAAGCAGATC
AAAAGAACAGAATAGACATAGATCTGATAAAACAAAAAGCAAGGGAAGCATTGAAGGAGTTAAAGAAAAAACAACCAGAA
GTAAGTCTAAGGAAAGAAAGAAGTCCAAGAGTCCATCTAAAAGAAGCAAATCCCAAGATCAAGCAAGAAAACCCAAATCC
CCAGGACTTAAAAGGCAATCTCAGGAGAAAATTGAAAAGGCCAAATCCCCTACTAAGGATAAGATTAAATTAGAAGATAA
AAGTAAATCAAAAGAAAGAAAGAAATCTCCAATTATAAATGAAAGCAAAAGTTGTGACCATGGGAAAAAATCCAAATCTC
CAATAGAACTAAGAAGCAAATCCAAAGACAGAAGGTCAAGATCCAAAGATAGAAAATCCCAAAGATCTGAGATTGACAAA
GAAAAGAAGCCAATTAAATCTCCCTCTAAAGGTGCTTCCTCTGGAAAAGAAAATAGGTCCCCAAGTAGAAGACCAGGTCG
TAGTCCTAAAGGAAAAAGTTCAACTCCAAAACAGCGTGATAAATCCAGAAGGAGTAGGTCCCCTCTACTTAATGATCAGA
GATCCAAGCTAAGTAAATCATCTCAAACTCTGCCTCCTGGTAGAAGAGCTAAGAGTCGATCAGTGGAAAGAAAACAAAGA
GAACCAGAAAGGAGAAGACTTTCTTCTACAAGAACACGTCCTAGGGATGATATTCTTAGCACACATGAGAGATCAAAAGA
TGTCAGTCCTATTAGCAGATGGTCCCCAACCAGAAGAAGATCAAGTAGGTCTCCTATCCGCAGGAGATCTTGTTCACCAC
TCAGGCAAAGCCGGTCTCCAAGGAGAAGAAGCAGGTCCCCAAGAAGAGATAGAAGTAGGCGGAGTAGATCTCGACTTCGA
TGGCGATCTCGACTTCGATGGCGATCTCGATCGAGGGGTGGTTGTAGGCGCAGAAGCAAAGTAAAGGAAGATAAATTTAC
AGGAAGCCTTTCTGAAGGGATGAAAGATGAACAGGAATCATCTGATGATAACCTAGAAGACCTTGATGTTGAAGAAGAAG
ATGAAGAAGCCCTAATAGAGAAGAGAAGACTCCAAAGGCAGGCAATTGTTCAGAAATATAAATACCTTGCTCAGGATAGC
AATATATCTATGCCATCTGAGCCAAGCAGCCCTCAGAGTAGCACTCGAACACGTTCACCGTCTCCTGATGACATTTTAGA
ATGGGTTGCTGCTGATGTTAAAGAATATGAAAGGGAAACTGTTGATACGTTTGAGGCCTCTGTAAAAGCCAAGCACAATC
TTATGACAGTTGAACAAAATGGTTCAACTCAGAAGAAACTATTGGCTCCTGACATGTTCACAGAATCAGATGATATGTTT
GCTGCATATTTTGATAGTGCTCATCTTCAGGCTGCTGGCATTGGAAAAGATTCCAAAGAAAATCCCAACCTCAGGGATAA
TTGGACTGATGCAGAAGGCTATTACCGTGTACACATAGGTGAAGTCCTAGAGAAAAGTTACACTGTGTATGGCTACACTG
GACAGGGTGTCTTCAGTAATGTAGTGAGAGCCAGAGACATGGCAAGAGCAAACCAGGAAGTGGCAGTGAAAATCATCAGG
AACAATGAGCTCATGCAAAAAACAGGGTTAAAAGAACTGGAATTTTTGAAAAAGCTTAATGATGCTGATCCTGATGACAA
ATTTCATTGTTTATGGCTCTTCAGACACTTTTACCATAAACAACATCTCTGCCTCGTGTTTGAGCCTCTAAGTATGAATT
TACGAGAGGTACTGAAAAAGTATGGAAAGGATGTCAGTCTCCATATTAAGGCTGTAAGATCCTATGGTCAGCAGTTGTTC
TTGGCATTGAAACTTCTTAAAAGGTGCAACATCCTACATGCTGATATTAAGCCAGACAATATCTTGGTTAATGAATCAAA
AACTATTCTAAAGCATTGTGACTTTGGATCAGCTTCACATGTTGCAGATAATGACATTACACCCTATCTCGTCAGTAGAT
TTTATCGTGCTCCTGAAATTATTATAGGAAAAAGCTATGACTATGGTATAGATATGTGGTCTGTAGGCTGCACATTATAT
GAACTTTATACTGGAAAAATATTATTTCCTGGTAAAACCAATAATCATATGTTGAAACTTGCTATGGACCTCAAAGGGAA
AATGCCAAATAAGATAAGAAAAGGTATGTTCAAAGAGCAGCACTTTGATCAAAATCTCAACTTCATGTACATAGAAGTAG
ATAAAGTAACAGAAAGGGAGAAAGTTACTGTCATGAGCACCATTAATCCTACCAAGGACCTGTTGGCTGATTTGATTGGG
TGCCAGAGGCTTCCTGAAGACCAACGCAAAAAAGTACACCAGCTAAAAGACTTGTTGGACCAGATCTTAATGTTGGACCC
AGCTAAACGAATTAGCACCCACCAGGCTCTACAGCATGCCTTCATCCAGGAAAAAATG

Alignment

ORF - retro_mdom_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.72 %
• Parental protein coverage: 89.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVIDASDKEGASPAKRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGYESGSEEEGEIH
          E.IDASDK.GASP.KRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGY.SGSEEEGEIH
Retrocopy EFIDASDKDGASPPKRTKIDDLALLEDLEKQRALIKAELDNELMEGKVQSGMGLILQGYDSGSEEEGEIH

Parental  EKARNGNRSTARSSNTKGKLELVDNKNSSKKRSKSRSKERTRHRSDKKKSKGSIEGVKEKTTRSKSKERK
          EK.RNGNRSTARSSNTK.KLELVDNK..SKK.SKSRSKE..RHRSDK.KSKGSIEGVKEKTTRSKSKERK
Retrocopy EKVRNGNRSTARSSNTKAKLELVDNKKHSKK*SKSRSKEQNRHRSDKTKSKGSIEGVKEKTTRSKSKERK

Parental  KSKSPSKRSKSQDQARKSKSPALKRRSQEKIGKAKSPTEDKIKLEDKSKSKDRKKSPIINESKSRDRGKK
          KSKSPSKRSKSQDQARK.KSP.LKR.SQEKI.KAKSPT.DKIKLEDKSKSK.RKKSPIINESKS.D.GKK
Retrocopy KSKSPSKRSKSQDQARKPKSPGLKRQSQEKIEKAKSPTKDKIKLEDKSKSKERKKSPIINESKSCDHGKK

Parental  SKSPIELRSKSKDRRSRSKDRKSKRSEIDKEKK----PIKSPSKDASSGKENRSPSRRP-GRS--PKGKS
          SKSPIELRSKSKDRRSRSKDRKS.RSEIDKEKK....P.K..S.........R.P.R.P.G.S..PK...
Retrocopy SKSPIELRSKSKDRRSRSKDRKSQRSEIDKEKKPIKSPSKGASSGKENRSPSRRPGRSPKGKSSTPKQRD

Parental  LSPKQRD---KSRRSRSPLLNDRRSKQSKSPSRTLSPGRRAKSRSVERKRREPERRRLSSPRTRPRDDIL
          .S...R.......RS................SR......R...R......R...R....S...R..D...
Retrocopy KSRRSRSPLLNDQRSKLSKSSQTLPPGRRAKSRSVERKQREPERRRLSSTRTRPRDDILSTHERSKD--V

Parental  SRRERSKDVSPISRWSPTRRRSSRSPIRRRSRSPLRRSRSPRRRSRSPRRRDRGRRSRSRLRRRSRSRGG
          S...R.......S..SP.RRRS..SP.R..SRSP.RRSRSPR.R.RS.RR................SRGG
Retrocopy SPISRWSPTRRRSSRSPIRRRSC-SPLRQ-SRSPRRRSRSPR-RDRS-RRSXXXXXXXXXXXXXXXSRGG

Parental  RRRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVEEEDEEALIEQRRIQRQAIVQKYKYLAEDSN
          .RRRS..KVKEDKF.GSLSEGMK.EQESS.DDN....................QRQAIVQKYKYLA.DSN
Retrocopy CRRRS--KVKEDKFTGSLSEGMKDEQESS-DDNXXXXXXXXXXXXXXXXXXXLQRQAIVQKYKYLAQDSN

Parental  MSMPSEPSSPQSSTRTRSPSPDDILERVAADVKEYERENVDTFEASVKAKHNLMTVEQNNGSTQKKLLAP
          .SMPSEPSSPQSSTRTRSPSPDDILE.VAADVKEYERE.VDTFEASVKAKHNLMTVEQN.GSTQKKLLAP
Retrocopy ISMPSEPSSPQSSTRTRSPSPDDILEWVAADVKEYERETVDTFEASVKAKHNLMTVEQN-GSTQKKLLAP

Parental  DMFTESDDMFAAYFDSARLRAAGIGKDFKENPNLRDNWTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSN
          DMFTESDDMFAAYFDSA.L.AAGIGKD.KENPNLRDNWTDAEGYYRV.IGEVL.K.Y.VYGYTGQGVFSN
Retrocopy DMFTESDDMFAAYFDSAHLQAAGIGKDSKENPNLRDNWTDAEGYYRVHIGEVLEKSYTVYGYTGQGVFSN

Parental  VVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPL
          VVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCL.LFRHFYHKQHLCLVFEPL
Retrocopy VVRARDMARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLWLFRHFYHKQHLCLVFEPL

Parental  SMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASH
          SMNLREVLKKYGKDV.LHIKAVRSY.QQLFLALKLLKRCNILHADIKPDNILVNESKTILK.CDFGSASH
Retrocopy SMNLREVLKKYGKDVSLHIKAVRSYGQQLFLALKLLKRCNILHADIKPDNILVNESKTILKHCDFGSASH

Parental  VADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN
          VADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN
Retrocopy VADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPN

Parental  KMIRKGVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL
          K.IRKG.FK.QHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL
Retrocopy K-IRKGMFKEQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLL

Parental  DQILMLDPAKRISINQALQHAFIQEKI
          DQILMLDPAKRIS..QALQHAFIQEK.
Retrocopy DQILMLDPAKRISTHQALQHAFIQEKM

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_1114 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1114 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000112739	1 retrocopy	retro_hsap_4212,
Gorilla gorilla	ENSGGOG00000006422	1 retrocopy	retro_ggor_2821,
Myotis lucifugus	ENSMLUG00000005901	1 retrocopy	retro_mluc_259,
Monodelphis domestica	ENSMODG00000009756	1 retrocopy	retro_mdom_1114 ,
Nomascus leucogenys	ENSNLEG00000011291	1 retrocopy	retro_nleu_1453,
Pan troglodytes	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859,