RetrogeneDB ID: retro_mdom_1955

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:16900391..16901878(+)
• 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_1955
CCCTGCCCCTGCGACTTCCCACTTGTCCCCCATTGCTTCCCTCTAACCACAACCACTGACAGACACCATGTCTGGACATC
AGAGTGGCAGAGAGCGCGGCAGGGATCGAGGCTTTGGGGCCCCGCGGTTTGGCGGAAGTAGAGGAGGACGTCCATCTGGA
AAGAAGTTTGGAAATGCTGGGGAGAAACTCCTTCACAAGAAATGGAACCCCGAGGAGCTTGAGAAGAATTTCTATCAGGA
ACACCTGATTTGGCGATGAGCACAGCACAAGAGGTTAAGACATATCGAAGAAGCAAAGAAATTTCATTTCGAGGTCACAA
GTCCCCAAAACCAGTTCCAAATTTCTATGAAGCCAACTTTCCTGCAAACGTCCTGGAAGTAATTGCAAGACAGAACTTTG
CCCAACCTCTTGCTATCCAAGCCCAGGGGTGTCCTGTTGCTCTAAGAGGGCTGCATCTGGTGGAGTAGCACAGACTGGAT
CAGGGAAAAGGCTGTCTTATTTGCTGCCTGCCATCGTGCACGTAAATCACCAGCCATTCCTAGAGAGAGGTGATGGGCCT
ATTTGTTTGGTGCTGGCGCCAACTCGTGAACTGGCCCAACAGGTACAAGGAGTAGCTGCTGCATACAGTAGAGCCTGTGG
TCTAAAACCCACCTGCATTTATGGTGGTGCTCCAAAGGGACCACAAAGACGGGACCTGGAAAGAGGGGCAGAAATGTGCA
TGGCCACACCTGGAAGACTGATAGACTCTTTAGAGTGCAGGAAAACAAATTTGAGAACTACTTACCTTGTACTTGATGAA
GCAGACAGAATGCTTGATATGGGCTTTGAGCCTCAAATCAGGAAAATTGTGGGTCAAATAAGACCTGGTAGACAAACCCT
ACTGTGGAGTGCCACGTGGCCAAAAGAAGTGAGGCAGCTTGCTGAAGACTTTTTGAAAGGTTATATTCAGATCAACATTG
GTGCTCTGGAACTGAGTGCCAACCGCAATATTCTTCAAATTGTGGATGTCTGTCATGATGGAGAAAAGGATGAGAAACTT
ATCCCATTGATGGAGGAGATCATGAGTGAAGGGGAAAATAAGAGGATTGTTTTTGTGGAAACCAAAAGAAGATGTGATGA
ACTTACCACAAAAATGAGGAGAGGTGGGTGGCCTGCAATGGGTGTCCATGGTGCCAAGAGTCAGGAGGAGGGAGACTGGG
TTCTAAATGAATTCAAAGATGGAAAAGCTCCTCTTCTGATTGCCACAGATGTTGCATCTAGAGGGCTAGATGTGGAAGAT
GTGAAATTTGTCATCAATTATGACTACCCCAACTCTTCAGAGGATTACATCCACCGAATTGGAGGAACTGCACCTTGGAC
CAAAACAGGCACAGCATAGACATTCTTTACACCTAATAACATAAAACAAGTAGGTGACCTCATCTCTGTGCTTCAGAAGG
CTAATCAAGCAATCAATCCCAAATTGCTTCAGTTGATTGAAGACAGG

Alignment

ORF - retro_mdom_1955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 73.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PFPCDFPLLLGCFPL-TAT-IDAMSGYSSDRDRGRDRGFGAPRFGGSRGGPLSGKKFGNPGEKLIKKKWN
          P.PCDFPL...CFPL.T.T..D.MSG..S.R.RGRDRGFGAPRFGGSRGG..SGKKFGN.GEKL..KKWN
Retrocopy PCPCDFPLVPHCFPLTTTT>TDTMSGHQSGRERGRDRGFGAPRFGGSRGGRPSGKKFGNAGEKLLHKKWN

Parental  LEELPKFEKNFYQEH-PDLARRTAQEVETYRRSKEITVRGHNCPKPILNFYEANFPANVMDVIARQNFTE
          .EEL...EKNFYQEH.PDLA..TAQEV.TYRRSKEI..RGH..PKP..NFYEANFPANV..VIARQNF..
Retrocopy PEEL---EKNFYQEH<PDLAMSTAQEVKTYRRSKEISFRGHKSPKPVPNFYEANFPANVLEVIARQNFAQ

Parental  PTAIQAQGWPVALSGLDMV-GVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQ
          P.AIQAQG.PVAL.GL..V.GVAQTGSGK.LSYLLPAIVH.NHQPFLERGDGPICLVLAPTRELAQQVQ.
Retrocopy PLAIQAQGCPVALRGLHLV<GVAQTGSGKRLSYLLPAIVHVNHQPFLERGDGPICLVLAPTRELAQQVQG

Parental  VAAEYSRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLD
          VAA.YSRAC.LK.TCIYGGAPKGPQ.RDLERG.E.C.ATPGRLID.LEC.KTNLR.TTYLVLDEADRMLD
Retrocopy VAAAYSRACGLKPTCIYGGAPKGPQRRDLERGAEMCMATPGRLIDSLECRKTNLR-TTYLVLDEADRMLD

Parental  MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEK
          MGFEPQIRKIV.QIRP.RQTL.WSATWPKEVRQLAEDFLK.YI.INIGALELSAN.NILQIVDVCHD.EK
Retrocopy MGFEPQIRKIVGQIRPGRQTLLWSATWPKEVRQLAEDFLKGYIQINIGALELSANRNILQIVDVCHDGEK

Parental  DEKLIRLMEEIMSEKENKTIVFVETKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPIL
          DEKLI.LMEEIMSE.ENK.IVFVETKRRCDELT.KMRR.GWPAMG.HG.KSQ.E.DWVLNEFK.GKAP.L
Retrocopy DEKLIPLMEEIMSEGENKRIVFVETKRRCDELTTKMRRGGWPAMGVHGAKSQEEGDWVLNEFKDGKAPLL

Parental  IATDVASRGLDVEDVKFVINYDYPNSSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQ
          IATDVASRGLDVEDVKFVINYDYPNSSEDYIHRIG.TA..TKTGTA.TFFTPNNIKQV.DLISVL..ANQ
Retrocopy IATDVASRGLDVEDVKFVINYDYPNSSEDYIHRIGGTAPWTKTGTA*TFFTPNNIKQVGDLISVLQKANQ

Parental  AINPKLLQLIEDR
          AINPKLLQLIEDR
Retrocopy AINPKLLQLIEDR

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_1955 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1955 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,