RetrogeneDB ID: retro_mdom_305

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:59737103..59738768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL16
• Ensembl ID: ENSMODG00000010765
• Aliases: METTL16, METT10D
• Description: methyltransferase like 16 [Source:HGNC Symbol;Acc:28484]

Sequence

>retro_mdom_305
ATGGCTTTGAATAAATCGATGCATGTTAGGAACAGGTACAAGGATAAGCCTCCTGACTTTGCATATCTGGCATCCAAGTA
CCCAGGTTTTAAGCAGCATGTCCGGATATATCTGACTGGAAGAGTCAGTCTTAACTTCAAAGACCCTGAAGCTGTCAGAT
CTTTGAATTGGACTCTCTTAAAAGGAGACTTTGGACTTTCCATTGATATTCCATTGGAAAGGCTCATTCCTCCGGTTCCA
CTTTGTCTCAATTATATTCACTGGGTGGAAGATCTGATTGGCTGTTGGGATGCAGCCAGAAGTGCCCATCACCAGGGGAT
TGACATTGGTACAGGAGCATCTTGCATCTATCCTTTACTTGGAGCAACTTTTAATGGCTGATATTTCCTTGCAACAGAAG
TGGATGATATGTGCTTTAATTATGCTAAGAAAACTGTGTAACAGAATAATTTATCTGATCTCATAAAAGTGGTTAAAGTA
CCACAGAAGACACTCCTAATGGATGCTCTTAAAGAGGAATCTGAGATCATTTATGATTTTTGCATGTGCAACCTCCTTTT
TTTGTCAACCAATTGGAAGTCAGGGGAATAAACTCTCGAAATCCTCGTAGGCCTCCCCCAAGTTCTGTAAACACTGGGGG
TATCACAGAAATCATGGCAGAAGGAGGTGAATTAGAGTTTGTCAAAAGAATCATCCCTTACAGTTTGCAGCTGAAGAAGA
GACTGAGATGGTACAGTTGCATGATTGGAAAGAAATGCTGTCTGGCTCCATTAATGGAAGAGCTTCACATACAAGGGGTC
CCCAAAGACACACACTGAATTCTTTCAGGGACACACAATGACATGGGCTTTGGCTTGGAGCTTTTATGATGGTGTGACAG
TACCTTAACCTCCATCTAAGAGAAGAAAATTAGAAAAACCAAGGCAGCCCATTACATTTGTGATCTTAGTAGCCACACTG
AAAGAGTTATCCCTCAAAGCTTCTGCTGCAGGCTCAGAGACTGTGGAAGGGATAGCAGTTATTACAACATGGCTTGAAAA
AATCCTCACTGATCTGAAGGTCCAGCATATAAGAGTTCCCTGTGGAAAGGAGGAAGTTAGTCTTTTCCTAACAGCTGTAG
AAAACTCTTGGGTTCATTTAAGGAGAAAGAAAAAAGAGAGTGAGGCAACTAAGAGAAATTCCTCGAGCCTCTGAAGACTT
CATCCAAGCTATGGAAGAGGAGAAACCCATGTCCAAAGAGATTGAAAATAACCCAGATGGGTCCAAGAGTACTGATGAGA
GCTCCCCACTCATGTCTGCCATGTGTGGAGCTGAAACAACTGTGTCTAAAAGTCACCATCCAGACCAAGGAGAAGTAGCC
TAGAGCCAGTGGAGGAAGGGACTGAGAAAAAGGTAACGACAGAGAACTTAGAATGTTCCAGGGGTTCTCTCTGTGCCACT
GAAGAGCTAGATGCTTCTGAAGAAGTCACCAATATAGTGACTCAAAAAGAGAAAAATTCTACAGGGACCCTTGGACATTA
TTTGTTTAAGTGTTTAATAAATGTCAAGAAGGAGGCAAACAATGATACAGTAATAGAAATGCATTGAGTTGAGGGCCAGA
ATAGGGATTTAATGAACCAGCTTTGTACATATTTACATAACCAGATTTTCAGGCTTGTTGCTAGT

Alignment

ORF - retro_mdom_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALNKSMHARNRYKDKPPDFAYLASKYPDFKQHVQINLTGRVSLNFKDPEAVRALTCTLLKEDFGLSIDI
          MALNKSMH.RNRYKDKPPDFAYLASKYP.FKQHV.I.LTGRVSLNFKDPEAVR.L..TLLK.DFGLSIDI
Retrocopy MALNKSMHVRNRYKDKPPDFAYLASKYPGFKQHVRIYLTGRVSLNFKDPEAVRSLNWTLLKGDFGLSIDI

Parental  PLERLIPTVPLRLNYIHWVEDLIGPWDPARSALRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFN
          PLERLIP.VPL.LNYIHWVEDLIG.WD.ARSA...GIDIGTGASCIYPLLGAT.NG.YFLATEVDDMCFN
Retrocopy PLERLIPPVPLCLNYIHWVEDLIGCWDAARSAHHQGIDIGTGASCIYPLLGATFNG*YFLATEVDDMCFN

Parental  YAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCN-PPFFANQLEAKGVNSRNPRRPPPSS
          YAKK.V.QNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCN.PPFF.NQLE..G.NSRNPRRPPPSS
Retrocopy YAKKTV*QNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCN<PPFFVNQLEVRGINSRNPRRPPPSS

Parental  VNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGV-PKVTHTEFCQG
          VNTGGITEIMAEGGELEFVKRII..SLQLKKRLRWYSCM.GKKC.LAPL.EEL.IQGV.PK.THTEF.QG
Retrocopy VNTGGITEIMAEGGELEFVKRIIPYSLQLKKRLRWYSCMIGKKCCLAPLMEELHIQGV>PK-THTEFFQG

Parental  RTMRWALAWSFYDDVTVPSPPSKRRKLEKPRKPITFVVLAATMKELSLKASAAGSETVEGIAVITTWLEK
          .TM.WALAWSFYD.VTVP.PPSKRRKLEKPR.PITFV.L.AT.KELSLKASAAGSETVEGIAVITTWLEK
Retrocopy HTMTWALAWSFYDGVTVP*PPSKRRKLEKPRQPITFVILVATLKELSLKASAAGSETVEGIAVITTWLEK

Parental  ILTDLKVQHKRVPCGKEEVSLFLTAVENSWVHLRRKKRD-RVRQLREVPRASEDFIQAMEEEKPMSKEIE
          ILTDLKVQH.RVPCGKEEVSLFLTAVENSWVHL.R.K...RVRQLRE.PRASEDFIQAMEEEKPMSKEIE
Retrocopy ILTDLKVQHIRVPCGKEEVSLFLTAVENSWVHL-RRKKK>RVRQLREIPRASEDFIQAMEEEKPMSKEIE

Parental  NNPDGSKSTDESSPLRPAMCGTETTVSKRHHPDQGD-SSQEPMEEGTEKKGRTENLECSRGSLCATEELD
          NNPDGSKSTDESSPL..AMCG.ETTVSK.HHPDQG..SS.EP.EEGTEKK..TENLECSRGSLCATEELD
Retrocopy NNPDGSKSTDESSPLMSAMCGAETTVSKSHHPDQGE<SSLEPVEEGTEKKVTTENLECSRGSLCATEELD

Parental  ASEEVTNTVAQKEKNSTGTLGHYLFKCLINVKKEANDDTVVEMHWVEGQNRDLMNQLCTYLRNQIFRLVA
          ASEEVTN.V.QKEKNSTGTLGHYLFKCLINVKKEAN.DTV.EMH.VEGQNRDLMNQLCTYL.NQIFRLVA
Retrocopy ASEEVTNIVTQKEKNSTGTLGHYLFKCLINVKKEANNDTVIEMH*VEGQNRDLMNQLCTYLHNQIFRLVA

Parental  S
          S
Retrocopy S

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_305 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_305 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017440	2 retrocopies	retro_btau_1159, retro_btau_1533,
Myotis lucifugus	ENSMLUG00000003531	2 retrocopies	retro_mluc_1130, retro_mluc_1625,
Monodelphis domestica	ENSMODG00000010765	2 retrocopies	retro_mdom_305 , retro_mdom_339,
Otolemur garnettii	ENSOGAG00000004504	1 retrocopy	retro_ogar_491,
Ictidomys tridecemlineatus	ENSSTOG00000011876	1 retrocopy	retro_itri_1568,