RetrogeneDB ID: retro_mdom_1956

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:16928876..16930082(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSMODG00000003743
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_mdom_1956
TATCGAAGAAGCAAAGAAATTTCATTTCGAGGTCACAAGGGCCCAAAACCAATTCTAAATTTCTATGAAGCCAACTTTCC
TGCAAACGTCCTGGATGTAATTGCAAGACAGAACTTTGCCCAACCTCCTGCTATCCAAGCCCAGGGGTGGCCTGTTGCTC
TAAGAGGGCTGCATCTGGTGGGAGTAGCACAGACTGGATCAGGGAAAAGGCTGTCTTATTTGCTGCCTGCCATCGTGCAC
GTAAATCACCAGCCATTCCTAGAGAGAGGTGATGGGCCTATTTGTTTGGTGCTGGCGCCAACTCGTGAACTGGCCCAACA
GGTCTAAGGAGTAGCTGCATACAGTAGAGCCTGTGGTCTAAAATCCACCTGCATTTATGGTGGTGCTCCAAAGGGACCAC
AAAGACGGGGCCTGGAAAGAGGGGCAGAAATGTGCATGGCCACACCTGGAAGACTGATAGACTCTTTAGAGTGCAGGAAA
ACAAATTTGAGAAGAACTACTTACCTTGTACTTGATGAAGCAGACAGGATGCTTGATATGGGCTTTGAGCCTCAAATCAG
GAAAATTGTGGGTCAGATAAGACCTGATAGACAAACCCTACTGTGGAGTGCCACGTGGCCAAAAGAAGCGAGGCAGCTGG
CTGAAGACTTTTTGAAAGATTATATTCATATCAACATTGGTGCCCTGGAACTGAGTGCAAAAAACAGTATTCTTCAGATT
GTGGATGTCTGTCATGATGGAGAAAAGGATGAGAAACTTATCCCATTGATGGAGGAGATCATGAGTGAAGGGGAAAATAA
GAGGATTGTTTTTGTGGAAACCAAAAGAAGATGTGATGAACTTACCACAAAAATGAGGAGAGGTGGGTGGCCTGCAATGG
GTGTCCATGGTGCCAAGAGTCAGGAGGAGGAAGACTGGGTTCTAAATGAATTCAAAGATGGAAAAGCTCCTCTTCTGATT
GCCACAGATGTTGCATCTAGAGGGCTAGATGTGGAAGATGTGAAATTTGTCATCAATTATGACTACCCCAACTCTTCAGA
GGATTACATCCACCGAATTGGAGGAACTGCACCTTGGACCAAAACAGGCACAGCATAGACATTCTTTACACCTAATAACA
TAAAACAAGTAGGTGACCTCATCTCTGTGCTTCAGGAGGCTAATCAAGCAATCAATCCCAAATTGCTTCAGTTGATTGAA
GACAGG

Alignment

ORF - retro_mdom_1956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 59.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YRRSKEITVRGHNCPKPILNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKT
          YRRSKEI..RGH..PKPILNFYEANFPANV.DVIARQNF..P.AIQAQGWPVAL.GL..VGVAQTGSGK.
Retrocopy YRRSKEISFRGHKGPKPILNFYEANFPANVLDVIARQNFAQPPAIQAQGWPVALRGLHLVGVAQTGSGKR

Parental  LSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYSRACRLKSTCIYGGAPKGPQIRDLE
          LSYLLPAIVH.NHQPFLERGDGPICLVLAPTRELAQQV..VAA.YSRAC.LKSTCIYGGAPKGPQ.R.LE
Retrocopy LSYLLPAIVHVNHQPFLERGDGPICLVLAPTRELAQQV*GVAA-YSRACGLKSTCIYGGAPKGPQRRGLE

Parental  RGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKE
          RG.E.C.ATPGRLID.LEC.KTNLRRTTYLVLDEADRMLDMGFEPQIRKIV.QIRPDRQTL.WSATWPKE
Retrocopy RGAEMCMATPGRLIDSLECRKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVGQIRPDRQTLLWSATWPKE

Parental  VRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKRRCD
          .RQLAEDFLKDYIHINIGALELSA...ILQIVDVCHD.EKDEKLI.LMEEIMSE.ENK.IVFVETKRRCD
Retrocopy ARQLAEDFLKDYIHINIGALELSAKNSILQIVDVCHDGEKDEKLIPLMEEIMSEGENKRIVFVETKRRCD

Parental  ELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDY
          ELT.KMRR.GWPAMG.HG.KSQ.E.DWVLNEFK.GKAP.LIATDVASRGLDVEDVKFVINYDYPNSSEDY
Retrocopy ELTTKMRRGGWPAMGVHGAKSQEEEDWVLNEFKDGKAPLLIATDVASRGLDVEDVKFVINYDYPNSSEDY

Parental  IHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLIEDR
          IHRIG.TA..TKTGTA.TFFTPNNIKQV.DLISVL.EANQAINPKLLQLIEDR
Retrocopy IHRIGGTAPWTKTGTA*TFFTPNNIKQVGDLISVLQEANQAINPKLLQLIEDR

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_1956 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1956 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956 ,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,