RetrogeneDB ID: retro_mdom_213

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:66520879..66522880(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025043
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013199
• Aliases: None
• Description: None

Sequence

>retro_mdom_213
ATGCAGAAGGAGCTCATCAGGCTTATTGCAGCAAAAAGAGAAAAGGAATATGTCAATTTTCATAACTTTAGGTTCTTTGT
TGGAACGTGGAATGTGAATGGCCAATCTCCAGACAGTGGGTTAGAACCGTGGCTGAATTGTGATAGAGACCCTCCAGACA
TTTACTGCCTTGGATTCCAAGAACTGGATTTGAGCATAGAGGCCTTCTTCTACTTTGAGTCTACCAAGGAGCATGAATGG
CTGGCATCCGTGAAAAGAGCTTTACACTTCAAGTCTAAGTATAATAAAGTACAGTTAGTCCGCCTGGTGGGAATGATGCT
ACTTATATTTGCCAGAAAGGAGCACTGTATGTATATCCAGGATGTTGTAACAGACACTGTGGGAACTGGGCTCATGGGGA
AAATGGGGAACAAAGGAGCTGTTGCTGTGAGATTTATGTTCCACAACACTACATTTTGCATTGTCAATTCCCACCTGGCT
GCTCAAATGGAAGATGTTGAAGGGCGGAATCAGGATTATAAGGACATCTGTGCTCGAATGAGTTTCCTTGTTCCAAATCA
GGGTCACCTGAATATCATGAAACATGATGTTGTCATTTGGTTAGGAGATTTGAACTACAGAATTTACATATATAGTGCCA
AAGAAGTAAAATGGCTTATTAGTAGGAATGACCTTCACAAGCTGCTAAAGCTAGACCAGCTGAATATTCAACGTTCAGAC
AAAAAAGCTTTTACTGACTTTACAGAAGGAGAAATTAGGTTTATCCCTACATATAAGTTTGACACTAAAACAGATAGATG
GGATTCCAGTGGGAAATGCCGGATTCCAGCATGGTGTGACCGAATTCTTTGGAAAGGGGAAAACATTCAGCAGCTCCGGT
ACCAAAGTCACATGGGGCTGAAAACCAGTGACCACAAACCTGTCAGTTCTTCTTTCCTCATTGGTGTGAAGGTTGTAAAT
AACAGTAAATACCAAGAGGTACTCAAAGACAGTGTTCAACTCATGGACAGAATGGAAAATTACTTTCTCCCTTCAATAGT
GCTTAGCAAGAGAGAATTTGTGTTTGAAAATGTGAAGTTTCAGCAACTGCAAAAGGAGAAATTCCAGATCACCAACAATG
GTCAGGTTCCCTGTCATTTTTCCTTCATCTCTAAGAATGGTGAGAGCCAGTACTGCAAACCATGGCTACAAGTTAACCCC
TGTCAGGGTTACTTGGAACCAAATGAGACATTAGACATTTCCTTGAGTGTCTATGTTAGTAAAGATTCTGTTCCAGTCCT
GAAATCGGGGGAAGAGAACATTAAAGACATTCTTATCCTTCACTTGGATCAAGGCAAAGATTACTTCTTGATCATCAGTG
GTAACTACCTCCGGAGTTGTTGCGGCACATCCCTGGAAGCATTATGCCAAATGAGAAGACCAATCAGAGAAGTTCCTGTT
TCCAAACTCATAGATTTGGAGATGACTCCTTTGGAAGAGAATGCCAGTGAAAAACCCCTTCAGATTCCCAAGGAACTCTG
GCTTTTAGTGGACCACTTATATAAGCATGCCTGTCACCAGAAGGACTTGTTCCAGACTCCTGGATCACAGAAAGAAGTTC
GGCAAATTATTGATTGTCTGGATACTAGCATTCCCAAGGCCATACCTGGCAGTAATTACTCAGTAGCTGAAACACTCCTT
ATCTTCTTGGAAGCTCTGCCAGAGCCTGTTGTCTGTTATGAACTATATCAAGACTGCCTTAACTATTCACATAACTTCCA
ACTCTGCCAAAAGGTAATTTCAGACCTTCCACAGTGTCATAGAAATGTTTTCTGGTGCCTAATAGCTTTCCTTCGAGAAC
TCTTGAGGCACTCTGAAAGTAACAATATTAATGCCAACATGCTTGCAAATCTCTTCTCAAGTCTTCTACTTCGGCCTCCA
CCTAACCTAAAGGCTAGACAGACTCAGACCAATCACCAGTGTGCTGTCCAGTTTCTCTTGGGCTTCTTGCTTGGAGGTGA
T

Alignment

ORF - retro_mdom_213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIRHILAKREKEYVNLQTFRFFIGTWNVNGQSPDSALEPWLNCDTDPPDIYCLGFQELDLSTEAFFYFES
          LIR.I.AKREKEYVN...FRFF.GTWNVNGQSPDS.LEPWLNCD.DPPDIYCLGFQELDLS.EAFFYFES
Retrocopy LIRLIAAKREKEYVNFHNFRFFVGTWNVNGQSPDSGLEPWLNCDRDPPDIYCLGFQELDLSIEAFFYFES

Parental  TKEQEWLTSVDRALHYKCKYKKVQLVRLVGMMLLIFAKKDQCKYLHDVVTETVGTGLMGKMGNKGAVAVR
          TKE.EWL.SV.RALH.K.KY.KVQLVRLVGMMLLIFA.K..C.Y..DVVT.TVGTGLMGKMGNKGAVAVR
Retrocopy TKEHEWLASVKRALHFKSKYNKVQLVRLVGMMLLIFARKEHCMYIQDVVTDTVGTGLMGKMGNKGAVAVR

Parental  FLFHNTTFCIVNSHLAAHVEDFERRNQDYKDICSRMTFSVPNQGHLNIMKHDVVIWLGDLNYRLCMPDAN
          F.FHNTTFCIVNSHLAA..ED.E.RNQDYKDIC.RM.F.VPNQGHLNIMKHDVVIWLGDLNYR.....A.
Retrocopy FMFHNTTFCIVNSHLAAQMEDVEGRNQDYKDICARMSFLVPNQGHLNIMKHDVVIWLGDLNYRIYIYSAK

Parental  EVKTLINRNELPKLLKLDQLNIQRSHKKAFADFTEGEIRFMPTYKFDPKTDRWDSSGKCRTPAWCDRILW
          EVK.LI.RN.L.KLLKLDQLNIQRS.KKAF.DFTEGEIRF.PTYKFD.KTDRWDSSGKCR.PAWCDRILW
Retrocopy EVKWLISRNDLHKLLKLDQLNIQRSDKKAFTDFTEGEIRFIPTYKFDTKTDRWDSSGKCRIPAWCDRILW

Parental  RGTNVNQQRYWSHMELKTSDHKPVSSLFLIGVKVVDDRRYRKVFEDSVRIMDRMENDFLPSLELSKREFV
          .G.N..Q.RY.SHM.LKTSDHKPVSS.FLIGVKVV....Y..V..DSV..MDRMEN.FLPS..LSKREFV
Retrocopy KGENIQQLRYQSHMGLKTSDHKPVSSSFLIGVKVVNNSKYQEVLKDSVQLMDRMENYFLPSIVLSKREFV

Parental  FEKVKFRQLQKQKFQVTNNGQVPCHFSFIPKLSDSQYCKPWLRAEPCEGYLEPNEMVDISLDVYVSKDSV
          FE.VKF.QLQK.KFQ.TNNGQVPCHFSFI.K...SQYCKPWL...PC.GYLEPNE..DISL.VYVSKDSV
Retrocopy FENVKFQQLQKEKFQITNNGQVPCHFSFISKNGESQYCKPWLQVNPCQGYLEPNETLDISLSVYVSKDSV

Parental  TLLNSGEDKIEDILVLHLDRGKDYFLTISGSYLPSCFGTSLEALCRMKRPIREVPVTKLIDL
          ..L.SGE..I.DIL.LHLD.GKDYFL.ISG.YL.SC.GTSLEALC.M.RPIREVPV.KLIDL
Retrocopy PVLKSGEENIKDILILHLDQGKDYFLIISGNYLRSCCGTSLEALCQMRRPIREVPVSKLIDL

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	0.12 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	595.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_213 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_213 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013199	1 retrocopy	retro_mdom_213 ,
Sarcophilus harrisii	ENSSHAG00000014095	1 retrocopy	retro_shar_100,