RetrogeneDB ID: retro_mdom_339

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:211332080..211333752(+)
• 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_339
ATGGCTTTGAATAAATCGATGCATGCAAGGAACAGGTACAAGGATAAGCCTCCTGACTTTGCATATCTGGCATCCAAGTA
CCCAGATTTTAAGCAGCATGTCCAGATAAATCTGACTGGAAGAGTCAGTCTTAACTTCAAGGACCCTGAAGCTGTCAGAG
CTTTGACTTGCACTCTCTTAAAAGAAGACTTTGGACTTTCCATTGATATTCCTTTGGAAAGGCTCATTCCTATGGTTCCA
CTTCGTCTCAACTATATCCACTGGGTGGAAGATCTGATTGGCCCTTGGGATCCAGCCAGGAGTGCCCTCCGCCGGGGGGA
TTGACATTGGTACAGGAGCATCTTGCATCTATCCTTTACTTGGAGCAACTCTCAATGGCTGGTATTTCCTTGCAACAGAA
ATGGATGATATGTGCTTTAATTATGCTAAGAAAAATGTGGAACAGAATAATTTATCTGATCTCATAAAAGTGGTTAAAGT
ACCACAGAAGACACTCCTAATGGATGCTCTTAAAGAGGAATCTGAGATCATTTATGATTTTTGCATGTGCAACCCTCCCT
TTTTTGCCAACCAGTTGGAAGCCAAGGGAGTAAACTCTCGAAATCCTTGTAGGCCTCCCCCAAGTTCTGTAAACACTGGG
GGTATCACAGAAATCATGGCAGAAGGAGGTGAATTAGAGTTTGTCAAAAGAATCATCCATGACAGTTTGCAGCTGAAGAA
GAGACTGAGATGGTACAGCTGCATGCTTGGAAAGAAATGCAGTCTGGCTCCATTGAAGGAAGAGCTTCGCATACAAGGGG
TCCCCAAAGTCAGGCACACTGAATTCTGTCAGGGGCGCACAATGAGATGGGCCTTGGCTTGGAGCTTTTATGATGATGTG
ACAGTACCTTCACCTCCATCTAAGAGAAGAAAATTAGAAAAACCCAGGAAGCCCATTACATTTGTGGTCTTAGCAGCCAC
AATGAAAGAGTTATCCCTCAAAGCTTCTGCTGCAGGCTCAGAGACTGTGGAAGGCATAGCAGTTATTACAACATGGCTTG
AAAAAATCCTCACTGATCTGAAGGTTCAGCATAAATGAGTTCCCTGTGGAAAAGAGGAAGTTAGTCTTTTCCTAACAGCT
GTAGAAAACTCTTGGGTTCATTTAAGGAGAAAGAAAAGAGACAGAGTGAGGCAACTGAGAGAAGTTCCTCGAGCCTCTGA
AGACTTCATCCAGGCTACGGAAGAGGAGAAACCCATGTCCAAAGAGATTGAAAATAACCCAGATGGGTCCAAGAGCACTG
ATGAGAGTTCCCCACTCAGGCCTGCCATGTGTGGAACTGAAACAACTGTGTCTAAAAGACATCATCCAGACCAAGGAGAC
AGTAGCCAAGAGCCAATGGAGGAAGGGACTGAGAAAAAGGGAAGGACAGAGAATTTAGAATGTTCCAGGGGTTCTCTCTG
TGCCACTGAAGAGCTAGATGCTTCTGAAGAAGTCACCAATACAGTGGCTCAAAAAGAGAAAAATTCTACAGGGACCCTTG
GACATTATTTGTTTAAGTGTTTAATAAATGTCAAGAAGGAGGCAAACGATGACACAGTAGTAGAGATGCATTGGGTTGAG
GGCCAGAATAGGGATTTAATGAACCAGCTTTGTACGTATTTACGCAACCAGATTTTCAGGCTTGTTGCTAGT

Alignment

ORF - retro_mdom_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALNKSMHARNRYKDKPPDFAYLASKYPDFKQHVQINLTGRVSLNFKDPEAVRALTCTLLKEDFGLSIDI
          MALNKSMHARNRYKDKPPDFAYLASKYPDFKQHVQINLTGRVSLNFKDPEAVRALTCTLLKEDFGLSIDI
Retrocopy MALNKSMHARNRYKDKPPDFAYLASKYPDFKQHVQINLTGRVSLNFKDPEAVRALTCTLLKEDFGLSIDI

Parental  PLERLIPTVPLRLNYIHWVEDLIGPWDPARSALRRG-IDIGTGASCIYPLLGATLNGWYFLATEVDDMCF
          PLERLIP.VPLRLNYIHWVEDLIGPWDPARSALRRG.IDIGTGASCIYPLLGATLNGWYFLATE.DDMCF
Retrocopy PLERLIPMVPLRLNYIHWVEDLIGPWDPARSALRRG>IDIGTGASCIYPLLGATLNGWYFLATEMDDMCF

Parental  NYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSS
          NYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNP.RPPPSS
Retrocopy NYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPCRPPPSS

Parental  VNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTHTEFCQGR
          VNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKV.HTEFCQGR
Retrocopy VNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVRHTEFCQGR

Parental  TMRWALAWSFYDDVTVPSPPSKRRKLEKPRKPITFVVLAATMKELSLKASAAGSETVEGIAVITTWLEKI
          TMRWALAWSFYDDVTVPSPPSKRRKLEKPRKPITFVVLAATMKELSLKASAAGSETVEGIAVITTWLEKI
Retrocopy TMRWALAWSFYDDVTVPSPPSKRRKLEKPRKPITFVVLAATMKELSLKASAAGSETVEGIAVITTWLEKI

Parental  LTDLKVQHKRVPCGKEEVSLFLTAVENSWVHLRRKKRDRVRQLREVPRASEDFIQAMEEEKPMSKEIENN
          LTDLKVQHK.VPCGKEEVSLFLTAVENSWVHLRRKKRDRVRQLREVPRASEDFIQA.EEEKPMSKEIENN
Retrocopy LTDLKVQHK*VPCGKEEVSLFLTAVENSWVHLRRKKRDRVRQLREVPRASEDFIQATEEEKPMSKEIENN

Parental  PDGSKSTDESSPLRPAMCGTETTVSKRHHPDQGDSSQEPMEEGTEKKGRTENLECSRGSLCATEELDASE
          PDGSKSTDESSPLRPAMCGTETTVSKRHHPDQGDSSQEPMEEGTEKKGRTENLECSRGSLCATEELDASE
Retrocopy PDGSKSTDESSPLRPAMCGTETTVSKRHHPDQGDSSQEPMEEGTEKKGRTENLECSRGSLCATEELDASE

Parental  EVTNTVAQKEKNSTGTLGHYLFKCLINVKKEANDDTVVEMHWVEGQNRDLMNQLCTYLRNQIFRLVAS
          EVTNTVAQKEKNSTGTLGHYLFKCLINVKKEANDDTVVEMHWVEGQNRDLMNQLCTYLRNQIFRLVAS
Retrocopy EVTNTVAQKEKNSTGTLGHYLFKCLINVKKEANDDTVVEMHWVEGQNRDLMNQLCTYLRNQIFRLVAS

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	2.86 RPM	0.00 RPM
SRP007412_cerebellum	1.96 RPM	0.00 RPM
SRP007412_heart	4.78 RPM	0.00 RPM
SRP007412_kidney	7.90 RPM	0.00 RPM
SRP007412_liver	2.01 RPM	0.00 RPM
SRP007412_testis	1.57 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_339 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_339 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,