RetrogeneDB ID: retro_mdom_747

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:309969249..309970611(+)
• Located in intron of: ENSMODG00000018714

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003708
• Aliases: None
• Description: None

Sequence

>retro_mdom_747
GAGGTTTACTTTGTTGATGCTTTCGACAAGGGAATGCTGGTTGGATGGGTTTTATCCAAAGCCAAGAAGGATGATACTGA
TGATGAAATTGCCAAATATGATGGTAAATGGAAAGTGGAAGAAATGAAGGAATCTAAACTTCCAGGAGATAAGGGGCTTG
TGTTGCTGTCATGAACCAAACATCATGTCATCTCTGCAAGGTTGAACAAGCCATTTACATTTGACACTAAGCCCCTCATT
GTTCAAAATGAAGTAGATTTCCAAAGTGGAATAGAATGTGGTGGAGCCTATGTGAAACTGCTTTCAAGAACTCCAGAATT
AAATCTGGATAAGTTCCATGACACGACCCTTTAAACAATAAAGTTTGGTCCAGATAAATGTGGAGAGGATTATAAGCTGC
ACTTCATCTTTAGACATAACAACCCAAAGACAGGCATCTATGAGAAAAAGCATGCTAAGAGACCAGATATGAATCTTAAG
ACCTACTTTACTGATAAGAAAACACATCTGTATACATTAGTCTTGAATCCAGATAATAGATTTGAAATATTAGTTGATCA
AATGTTTGGGAATAGTGGGAACCTTCTGAATGATATCACTCTTTCTGTGAATCCTCCCCAGGAAATTGAGGATCGAAATG
ACTAGAAACCTGAGGACTGGGATGAGAGCCCGAAGATACCAGATCCTGATCTTATCAAACAAGATGACTGTGATGAGACT
GTTCCTGCTAAGATTCCAGATGAGGATGCTACAAAACCTGAAGGCTGGTTGGATGATGAACCTGAATATGTATCTGATCC
AGATGCAGAGAAGCCAGAGGATTGGGATGAAGATATGGATGGAGAATGGGAAGCTCCCCAAATTGCAAACCCAAAATGTG
AATCAGCCCCTGATTGTTGGGATGTAATTGGGATTAACAATCCCAATTACAAGGGCAAATGGAAAGCACCTATGATTGAC
AATCCTAAATACCAAGGAATCTGGAAACCAAGGAAGACTCCAAACCCAGGTTTCTTTGAAGATCTAGAGCCTTTCAAAAT
GACTCCTTTCAGTGCTGTGGGTCTGGAGCTGTGGTCCATGACATCAAATATCTTCTTTGACAACTTCATTATTTGTGCAG
GCTGAGCAGTTGCAGATGATTGGGTCAATTATGGGTGGGGTCTGAAGAAAGCTGCTGATGAGACTGAAGAGCCTGGTGTA
ATGGGACAAATGCTTGAAGCAGCTTAAGAATGTCCATGGCTTTGGGTGGTTTATATTCTCGCTGTGGCCTTGCCATTGTT
CCTTGCAGTCCTCTTCTGCTGTTCTGGAAACAAACAACCTAAAGCTGCAGAGCATAAGAAGACAGATGATCCTCAACTAG
AT

Alignment

ORF - retro_mdom_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.28 %
• Parental protein coverage: 81.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVYFVDAFDKGMLVGWVLSKAKKDDTDDEIAKYDGKWEVEEMKESKLPGDKGLVLLSRAKHHAISARLNK
          EVYFVDAFDKGMLVGWVLSKAKKDDTDDEIAKYDGKW.VEEMKESKLPGDKGLVLLS..KHH.ISARLNK
Retrocopy EVYFVDAFDKGMLVGWVLSKAKKDDTDDEIAKYDGKWKVEEMKESKLPGDKGLVLLS*TKHHVISARLNK

Parental  PFTFDTKPLIVQYEVNFQSGIECGGAYVKLLSRTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHK
          PFTFDTKPLIVQ.EV.FQSGIECGGAYVKLLSRTPELNLD.FHD.T..TI.FGPDKCGEDYKLHFIFRH.
Retrocopy PFTFDTKPLIVQNEVDFQSGIECGGAYVKLLSRTPELNLDKFHDTTL*TIKFGPDKCGEDYKLHFIFRHN

Parental  NPKTGIYEEKHAKRPDTDLKTYFTDKKTHLYTLVLNPDNSFEILVDQMVVNSGNLLNDMTPPVNPPREIE
          NPKTGIYE.KHAKRPD..LKTYFTDKKTHLYTLVLNPDN.FEILVDQM..NSGNLLND.T..VNPP.EIE
Retrocopy NPKTGIYEKKHAKRPDMNLKTYFTDKKTHLYTLVLNPDNRFEILVDQMFGNSGNLLNDITLSVNPPQEIE

Parental  DPNDQKPEDWDERPKIPDPDAVKPDDWDETAPAKIPDEDATKPEGWLDDEPEYVSDPDAEKPEDWDEDMD
          D.ND.KPEDWDE.PKIPDPD..K.DD.DET.PAKIPDEDATKPEGWLDDEPEYVSDPDAEKPEDWDEDMD
Retrocopy DRND*KPEDWDESPKIPDPDLIKQDDCDETVPAKIPDEDATKPEGWLDDEPEYVSDPDAEKPEDWDEDMD

Parental  GEWEAPQIANPKCESAPGCGVWQRPTIDNPNYKGKWKAPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMT
          GEWEAPQIANPKCESAP.C..W....I.NPNYKGKWKAPMIDNP.YQGIWKPRK.PNP.FFEDLEPFKMT
Retrocopy GEWEAPQIANPKCESAPDC--WDVIGINNPNYKGKWKAPMIDNPKYQGIWKPRKTPNPGFFEDLEPFKMT

Parental  PFSAVGLELWSMTSDIFFDNFIICADRAVADDWANDGWGLKKAADGAAEPGVMGQMLEAAEERPWLWVVY
          PFSAVGLELWSMTS.IFFDNFIICA..AVADDW.N.GWGLKKAAD...EPGVMGQMLEAA.E.PWLWVVY
Retrocopy PFSAVGLELWSMTSNIFFDNFIICAG*AVADDWVNYGWGLKKAADETEEPGVMGQMLEAA*ECPWLWVVY

Parental  ILTVALPLFLVVLFCCSGKKQPSAAEYKKTDAPQPD
          IL.VALPLFL.VLFCCSG.KQP.AAE.KKTD.PQ.D
Retrocopy ILAVALPLFLAVLFCCSGNKQPKAAEHKKTDDPQLD

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	1646.82 RPM
SRP007412_cerebellum	0.00 RPM	1522.26 RPM
SRP007412_heart	0.00 RPM	783.05 RPM
SRP007412_kidney	0.00 RPM	2795.64 RPM
SRP007412_liver	0.00 RPM	1890.60 RPM
SRP007412_testis	0.00 RPM	1046.79 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_747 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_747 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003708	2 retrocopies	retro_mdom_1933, retro_mdom_747 ,
Drosophila melanogaster	FBgn0015622	2 retrocopies	retro_dmel_33, retro_dmel_50,