RetrogeneDB ID: retro_mdom_1667

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:98402164..98403415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018427
• Aliases: None
• Description: None

Sequence

>retro_mdom_1667
TTTGGGACTGCTCATTTAGGAACAGGTGCTCCCTTTACACCTGGATTCCTTTCCTTCAACCACACTCAATTCCCACCATC
ACAGTTATCAGGATTACCTACTATTCCTGTCCAAACAATCTCTACATCACAGGTGGTGAAACTCTTCAGTAAAATGGATG
GTGCTGACTGCCCCTGAGGCTGGGATAAGGATAGTAAATATAAGATAAGCCCAAGAGTGAATGTGAGGCTGTCAACAATG
TACTAGAAGAAAAACAACTTCTCTATATTTTTGGAGTTGTCAAAGGTATTGATGAACCAGATCACTATGTTGTCATAGGG
GTCCAGAGGGATGCCCGGGCCCTGGGGCTGCCAAATCTCTGGTGGGGACATCTCTTCTTCTAGAGGTTGCTCGTGCTTAT
TCTGATTTGGTGAAAGATGGGTATAAACCCAGAAGAAGTATTGTCTTTGCCGGCTGGACTGGTAGAGAATTTGGAGCTGT
TGGTGCCCCTGAATGGCTAGAGGGTTTACCTTTCCACATTGCATCAAAAGGCCATCACGCACATAAACCTGGATACTGCA
GTACTTAGTTCAAGTAACTTCAAAGTTTTTGCCACTCCATTGTTGTATAAGCTCATTGAGAAGACCACGAAAGACGTGAA
CCATCCAGTTACAGGAGCAGCTCTCTTCAGAGACACTCCCTGGACCAGTGAGGTGGGACCACTTACATTGGATAATGCTA
CTTATCCTTTTCTTGCTTATTCTGGAATCCCATCAGTTTCATTTTGGTTTTGGGAGAATAAGGCTTATCAGTACTTGGGC
ACCAGCTTGGATTCTTATAATGAACTGATAAAAAGTATTCCTAAACTGAAAAAAACTGATGCACGGAGCTGAAGAAGTGA
CTAGCCAAATGGTGATTAGGCTCACATGTGGCCATGAGTTGTACCTAAACTATGAAAGGTACCATGAAGAAGTATTCAGT
TTTGTAAAGAAACTTGTGCCTTACATGACAAATTTAAAGGAAATGAATCTGAGTTTGCAGTGACTCTGCTCTGCTCATGG
TGACTTTAGCAGGGCTTCTTGTGACCTGACAAATGACCTATATTGTACAGATGCTGCCAACAGACTCGTTAATAGAGAAA
TCAATGACCATATCATGAAAGTGGAATCCAGCTTCCTTTCTCCCTATGTCTCTCCAAAGGAAAGTCCTTTTCGACATATC
TTTTGGGGATCTGGCTCTCGTCCTCTTTCAGCTTTGTTAGATCATATTCGG

Alignment

ORF - retro_mdom_1667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 65.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FGHAHLGTGDPFTPGFPSFNHTQFPPSQSSGLPTIPVQTISRSQALKLF-RMNGADCPQGWDGDSKCKIS
          FG.AHLGTG.PFTPGF.SFNHTQFPPSQ.SGLPTIPVQTIS.SQ..KLF..M.GADCP.GWD.DSK.KIS
Retrocopy FGTAHLGTGAPFTPGFLSFNHTQFPPSQLSGLPTIPVQTISTSQVVKLFSKMDGADCP*GWDKDSKYKIS

Parental  SEVNVRLTV-NNVLEERKLLNIFGVVKGIDEPDRYVVIGAQRDAW-GPGAAKSLVGTSLLLEVARAYSDL
          ..VNVRL...N...E...LL.IFGVVKGIDEPD.YVVIG.QRDA..GPGAAKSLVGTSLLLEVARAYSDL
Retrocopy PRVNVRLST<NVLEEKQ-LLYIFGVVKGIDEPDHYVVIGVQRDAR<GPGAAKSLVGTSLLLEVARAYSDL

Parental  VKGGYKPRRSVVFASWSGGEFGAVGATEWLEG-YLSTLHQKAITYINLDTAVLGSSNFKVSASPLLYTLI
          VK.GYKPRRS.VFA.W.G.EFGAVGA.EWLEG.YLSTLHQKAIT.INLDTAVL.SSNFKV.A.PLLY.LI
Retrocopy VKDGYKPRRSIVFAGWTGREFGAVGAPEWLEG>YLSTLHQKAITHINLDTAVLSSSNFKVFATPLLYKLI

Parental  EKTMKEVNHPVTGTALFRDTNWISEVEPLTLDNAAYPFLAYSGIPSVSFCFCENKAYKYLGTSLDSYNEL
          EKT.K.VNHPVTG.ALFRDT.W.SEV.PLTLDNA.YPFLAYSGIPSVSF.F.ENKAY.YLGTSLDSYNEL
Retrocopy EKTTKDVNHPVTGAALFRDTPWTSEVGPLTLDNATYPFLAYSGIPSVSFWFWENKAYQYLGTSLDSYNEL

Parental  IKSIPQL-KKLMYGAAEVTSQMVIRLTRDHELYLDYERYNEELFSFVKKLVPYMSNLKEMNLSLQWLFSA
          IKSIP.L.KKLM.GA.EVTSQMVIRLT..HELYL.YERY.EE.FSFVKKLVPYM.NLKEMNLSLQ.L.SA
Retrocopy IKSIPKL>KKLMHGAEEVTSQMVIRLTCGHELYLNYERYHEEVFSFVKKLVPYMTNLKEMNLSLQ*LCSA

Parental  RGDFSRATRDLTNDLFRTDTANRLVNREINDRIMKVEYSLLSPYVSPKESPFRHIFWGSGSHTLSALLDH
          .GDFSRA..DLTNDL..TD.ANRLVNREIND.IMKVE.S.LSPYVSPKESPFRHIFWGSGS..LSALLDH
Retrocopy HGDFSRASCDLTNDLYCTDAANRLVNREINDHIMKVESSFLSPYVSPKESPFRHIFWGSGSRPLSALLDH

Parental  IK
          I.
Retrocopy IR

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_1667 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1667 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018427	1 retrocopy	retro_mdom_1667 ,