RetrogeneDB ID: retro_mdom_39

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:23545514..23547266(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000020561
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007003
• Aliases: None
• Description: None

Sequence

>retro_mdom_39
ATGACAGCAGATTCCGCTACAAAGATGAGCAATGATTCCACCAACGCGGCGGCAGCCAAAGCTCCTGAAGGTGTAGCCGG
GGCACCTAATGAGGCTGCCCTGTTGGCTCTCATGGAGCGCACGGGCTACAGTATGACACAGGAAAACGGTCAGCGCAAGT
ATGGTGGTCCTCCCCCTGGATGGGAAGGGCTGCACCCCCCGCGTGGCTGTGAGGTCTTCGTGGGTAAAATTCCCCGAGAC
GTGTATGAAGACGAGCTGGTTCCAGTGTTTGAGTCCGTGGGGCGTATCTACCAGATGCGACTGATGATGGACTTTGATGG
GAAGAACCGCGGCTACGCTTTTGTCATGTATACTCACAAGCGCGAAGCCAAGCGGGCCGTGAGGGAACTGGACAATCATG
AAATCAGACCGGGTCGACCTCTGGGAGTCTGTTGCAGTGTGGATAACTGCCGACTCTTCATCGGTGGCATCCCTAAGATG
AAAAAGAGAGACGAGATCCTGGAAGAGATCTCTAAGGTGACCGAAGGGGTTCTAGACGTTATCGTGTACGCAAGTGCCAC
GGATAAGACGAAGAACAGAGGGTTTGCCTTCATAGAGTACGAGAGCCACCGGGCAGCGGCCATGGCCAGGAGAAAGCTCA
TGCCTGGAAGGATCCAGCTGTGGGGACAGCAGATCGCGGTGGACTGGGCAGAGCCAGAGATGGATGTCGACGAAGATGTC
ATGGAAACCGTTAAGATCCTGTACGTGAGAAATCTGATGATCAAAACCAGCGAGGAGACGATCAGAAAGACCTTCAGCCA
GTTTGGCTGTGTGGAACGAGTCAAAAAGATCCGCGATTACGCATTTGTTCACTTCACCAGCCGGGAAGATGCCATCCGTG
CTATGAACAGCCTCAATGGCACCGAGCTCGAAGGCTCGTGTCTTGGAGTTACTTTGGCCAAACCAGTAGACAAAGAGCAA
TACGCACGCTATCGGAAGGCAGTCAAAGGAAGTGTGACAGCAGAAGTCCAGCAGCTCAACTATGTTTACTCGTGCGATCC
CTATACTTTGGCCTACTACAGCTATCCCTACAGTGCTCTCTTTGGGCCCAACAGAGATTATTTTGTGAAGGCAGAGAGCG
TGAGAGGCCGAGGGCAAGACACAGCTGGCAGCAGAGCCCCGGGCCCCAGGGGATCCTACTTCGGGGGGTACTCTGCAGGC
CGTGGCATCTATAGCCGATATCATGAGGGGAAAGGAAAGTGGCGAGAAAGAGGATATGAGTTTGTACCGAACTTGGAATT
ATCTGCCGCCAATCCAGTTCCTATTAAACCCGGTACAGTGGCAATCCCTGCTCTTGGCGCCCAGTATTCCATGTTTCAGG
CTGGCCCTGCTCCCAAGTTGCTGGAAGATGGCAAAATGCATGCAATGGAACACATGATCAACCCCATAGCAGTACAAGCA
GACCCAGCCGGTGCCTCTGCTGCCGCCGCCGCTGCCACCATACCTGCTGGTTCCACCCCTCCACCTTTCCAGGCACGCCC
GATAACTCCAGTATTCACAGGGGCTCCAAACGTCCAGAGAATTCCCGCGGCTGGGCTCTACGGTGCCGGTTACATCCCCT
TTGCTGCTCCTGCCTCAGCCACATCAGCCACAGTACAGAAGAGCGCCGCAGCCACAGCTCCCGTTTATGGAGGTTATGGT
GGCTATATTCCTCAGCCATTCCCTTCGGCTACCATTCAGCCTCCCATACACGAAGACTACCAGACATACTGA

Alignment

ORF - retro_mdom_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTAEDSTTTMSNDSTNVSAAKVPEGIAGAPNEAALLALMERTGYSMIQENGQRKYGGPPPGWEGLHPPRG
          MTA.DS.T.MSNDSTN..AAK.PEG.AGAPNEAALLALMERTGYSM.QENGQRKYGGPPPGWEGLHPPRG
Retrocopy MTA-DSATKMSNDSTNAAAAKAPEGVAGAPNEAALLALMERTGYSMTQENGQRKYGGPPPGWEGLHPPRG

Parental  CEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTHKHEAKRAVRELNNYEIRPGR
          CEVFVGKIPRDVYEDELVPVFESVGRIY.MRLMMDFDGKNRGYAFVMYTHK.EAKRAVREL.N.EIRPGR
Retrocopy CEVFVGKIPRDVYEDELVPVFESVGRIYQMRLMMDFDGKNRGYAFVMYTHKREAKRAVRELDNHEIRPGR

Parental  LLGVCCSVDNCRLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA
          .LGVCCSVDNCRLFIGGIPKMKKR.EILEEISKVTEGVLDVIVYASA.DK.KNRGFAF.EYESHRAAAMA
Retrocopy PLGVCCSVDNCRLFIGGIPKMKKRDEILEEISKVTEGVLDVIVYASATDKTKNRGFAFIEYESHRAAAMA

Parental  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEETIKKSFGQFNPGCVERVKKI
          RRKLMPGRIQLWG.QIAVDWAEPE.DVDEDVMETVKILYVRNLMI.T.EETI.K.F.QF..GCVERVKKI
Retrocopy RRKLMPGRIQLWGQQIAVDWAEPEMDVDEDVMETVKILYVRNLMIKTSEETIRKTFSQF--GCVERVKKI

Parental  RDYAFVHFTSREDAVHAMNSLNGTELEGSCLEVTLAKPVDKEQYTRYQKAAKGSATAEVTPQQPNYVYSC
          RDYAFVHFTSREDA..AMNSLNGTELEGSCL.VTLAKPVDKEQY.RY.KA.KGS.TAEV..QQ.NYVYSC
Retrocopy RDYAFVHFTSREDAIRAMNSLNGTELEGSCLGVTLAKPVDKEQYARYRKAVKGSVTAEV--QQLNYVYSC

Parental  DPYTLAYYSYPYNALIGPNRDYFVKAGSVRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQ
          DPYTLAYYSYPY.AL.GPNRDYFVKA.SVRGRG...AG.RAPGPRGSY.GGYSAGRGIYSRYHEGKGK..
Retrocopy DPYTLAYYSYPYSALFGPNRDYFVKAESVRGRGQDTAGSRAPGPRGSYFGGYSAGRGIYSRYHEGKGKWR

Parental  EKGYELVPNLELSAVNPVPIKPGTVAIPAIGAQYSMFQTAPAPKMLEDGKIHTMEHMINPIAVQPDPASA
          E.GYE.VPNLELSA.NPVPIKPGTVAIPA.GAQYSMFQ..PAPK.LEDGK.H.MEHMINPIAVQ.DPA.A
Retrocopy ERGYEFVPNLELSAANPVPIKPGTVAIPALGAQYSMFQAGPAPKLLEDGKMHAMEHMINPIAVQADPAGA

Parental  AAAAAAAAAAAVMPAVSTPPPFQGRPITPVYTVAPNVQRIPAAGIYGASYVPFAAPASATLATIQKSAAA
          .AAAAAA......PA.STPPPFQ.RPITPV.T.APNVQRIPAAG.YGA.Y.PFAAPASAT.AT.QKSAAA
Retrocopy SAAAAAA----TIPAGSTPPPFQARPITPVFTGAPNVQRIPAAGLYGAGYIPFAAPASATSATVQKSAAA

Parental  AAAVYGGYGGYIPQPFPTATIQVPIHDVYQTY
          .A.VYGGYGGYIPQPFP.ATIQ.PIH..YQTY
Retrocopy TAPVYGGYGGYIPQPFPSATIQPPIHEDYQTY

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_39 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_39 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000007003	1 retrocopy	retro_mdom_39 ,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Otolemur garnettii	ENSOGAG00000029367	1 retrocopy	retro_ogar_273,