RetrogeneDB ID: retro_mdom_1933

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:187126867..187128482(-)
• Located in intron of: None

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_1933
ATGGAACCAAAGTGGTGGTTATTTATGGTTTTGCTGCTCCTTGGAACAGTGGTTCAGGCACATGATGGACATGCTGATGA
AGATGATGATGATGAGGAGGACAATGATGTAATTGATGTAGAAGAAGACCTAGAAGATGGCATTGAGGAAATAGAAGACT
CAAAGCCTGGAGATGGTGCCACTCTTCCTCCATCACCAAAGGTTATCTACAAAGCCCTGGTTCCAACAGGAGAGGTTTAC
TTTGTTGGTGCCTTTGACAAGGGAATGCTGGTTGGATGGGTTTTATCCAAAGTCAAGAAGGATGATACTGATGATGAAAT
TGCCAAATATCTTAAATGGGAAAGTATCTGTAAATGGGAAGTGGAAGAAATGAAGGAATCTAAACTTCCAGGAGATAAGG
GACTTGTGTTGCTCTCATGAGCCAAACATCATGCCATCTCTGCAAGGTTGAACAAGGCATTTGGCATTTGACACTAAGTC
CCTCGTTGTTCAGTATGAAGTAAATTTCCAAAGTGGAATAGAATGTGGTGGAGCCTATGTGAAACTGCTTTCAAGAACTC
CAGAATTAAATCTGGATCACTTCCACAACAAGACCCCTTACACAATAATGTTTGGTCCAGATAAATGTGGAGAGGACTAT
AAGTTGCACTTCATTTTCAGGCATAAAAACCCAAAGACAGACATTGATGAGGAAAAGTATGCTAAGAGACCAGATATGGA
TCTGAAGACCTACTTTACTGATAAGAAAACACATCTGTATACATTAGTCTTGAATCCAGATAATAGCTTTGAAATATTAG
TTGATCAAATGGTTGTGAATAGTGGGAACCTTCTGAATGATATGACTCCTCCTGTGAATCCTTCCCGGGAAATTGAGAAT
CCAAATGACCAGAAGCCTGAGGACTGGGATGAAAGGCTGAAGATACCAGATCCTGATGCTGTCAAACTAGATGACTGGGA
TGACACTGCTTCTGCTAAGATTCCAGATAAGGATGCTACAAAACCTGAAGGCTGGTTGGATGATGAGCCTGAATATGTAT
CTGATCCAGATGCAGAGAAGCCAGAGGATTGGGATGAAGATATGAATGGAGAATGGGAAGCTCCCCAAATTGCAAACCCA
AAATGTGAATAAGCCTCTGGTTGTGATGTCTGGCAAAGACCTACCACTGACAATCCCAATTAAAAGGGCAAATGGAAAGC
ACCTATGATTGACAATCCTAACTGCCAGGGAATCTGGAAACCAAGGAAGATTCCAAACCCAGATTTCTTTGAAGATCTAG
AGCCTTTCAAAATGACTCCTTTCAGTGCTGTGGGTCTGGAGCTGTGGTCCATGACATCAGATATCTTCTTTGACAATTTT
ATTATTTGTGCAGACTGAGCAGTTGCAGATGACTGGGCCAATGATGGTTGGGGTCTGAAGAAAGCTGCTGATGGGGCTGC
AGAGCCTGATGAAATGGGGCAAATGCTTGAAGCAGCTGAAGAATGTCCATGGCTTTGGGTGGTCTATATTCTTATTGTGG
CCTTGCCATTGTTCCTTGTGGTCCTCTTCTGCTGTTCTGGAAAGAAACAACCTTGTGCTGCAGAGTATAAGAAGACAGAT
GCTCCTCAACCAGAT

Alignment

ORF - retro_mdom_1933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 95.01 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPKWWLFMVLLLLGTVVQAHDGHDDEDDDDDEDDDVIDVEEDLEDGIEEVEDSKLGDGVTFPPSPKVTY
          MEPKWWLFMVLLLLGTVVQA.................IDVEEDLEDGIEE.EDSK.GDG.T.PPSPKV.Y
Retrocopy MEPKWWLFMVLLLLGTVVQAXXXXXXXXXXXXXXXXXIDVEEDLEDGIEEIEDSKPGDGATLPPSPKVIY

Parental  KAPVPTGEVYFVDAFDKGMLVGWVLSKAKK---DDTDDEIAKYDG--KWEVEEMKESKLPGDKGLVLLSR
          KA.VPTGEVYFV.AFDKGMLVGWVLSK.KK...DD......K.....KWEVEEMKESKLPGDKGLVLLS.
Retrocopy KALVPTGEVYFVGAFDKGMLVGWVLSKVKKDDTDDEIAKYLKWESICKWEVEEMKESKLPGDKGLVLLS*

Parental  AKHHAISARLNKPF-TFDTKPLIVQYEVNFQSGIECGGAYVKLLSRTPELNLDQFHDKTPYTIMFGPDKC
          AKHHAISARLNK.F..FDTK.L.VQYEVNFQSGIECGGAYVKLLSRTPELNLD.FH.KTPYTIMFGPDKC
Retrocopy AKHHAISARLNKAF>AFDTKSLVVQYEVNFQSGIECGGAYVKLLSRTPELNLDHFHNKTPYTIMFGPDKC

Parental  GEDYKLHFIFRHKNPKTGIYEEKHAKRPDTDLKTYFTDKKTHLYTLVLNPDNSFEILVDQMVVNSGNLLN
          GEDYKLHFIFRHKNPKT.I.EEK.AKRPD.DLKTYFTDKKTHLYTLVLNPDNSFEILVDQMVVNSGNLLN
Retrocopy GEDYKLHFIFRHKNPKTDIDEEKYAKRPDMDLKTYFTDKKTHLYTLVLNPDNSFEILVDQMVVNSGNLLN

Parental  DMTPPVNPPREIEDPNDQKPEDWDERPKIPDPDAVKPDDWDETAPAKIPDEDATKPEGWLDDEPEYVSDP
          DMTPPVNP.REIE.PNDQKPEDWDER.KIPDPDAVK.DDWD.TA.AKIPD.DATKPEGWLDDEPEYVSDP
Retrocopy DMTPPVNPSREIENPNDQKPEDWDERLKIPDPDAVKLDDWDDTASAKIPDKDATKPEGWLDDEPEYVSDP

Parental  DAEKPEDWDEDMDGEWEAPQIANPKCESAPGCGVWQRPTIDNPNYKGKWKAPMIDNPNYQGIWKPRKIPN
          DAEKPEDWDEDM.GEWEAPQIANPKCE.A.GC.VWQRPT.DNPN.KGKWKAPMIDNPN.QGIWKPRKIPN
Retrocopy DAEKPEDWDEDMNGEWEAPQIANPKCE*ASGCDVWQRPTTDNPN*KGKWKAPMIDNPNCQGIWKPRKIPN

Parental  PDFFEDLEPFKMTPFSAVGLELWSMTSDIFFDNFIICADRAVADDWANDGWGLKKAADGAAEPGVMGQML
          PDFFEDLEPFKMTPFSAVGLELWSMTSDIFFDNFIICAD.AVADDWANDGWGLKKAADGAAEP..MGQML
Retrocopy PDFFEDLEPFKMTPFSAVGLELWSMTSDIFFDNFIICAD*AVADDWANDGWGLKKAADGAAEPDEMGQML

Parental  EAAEERPWLWVVYILTVALPLFLVVLFCCSGKKQPSAAEYKKTDAPQPD
          EAAEE.PWLWVVYIL.VALPLFLVVLFCCSGKKQP.AAEYKKTDAPQPD
Retrocopy EAAEECPWLWVVYILIVALPLFLVVLFCCSGKKQPCAAEYKKTDAPQPD

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_1933 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1933 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 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,