RetrogeneDB ID: retro_mdom_296

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:13804214..13805636(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005221
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006919
• Aliases: None
• Description: None

Sequence

>retro_mdom_296
TCTCTTACCAGGGGAGCCAAGATGAGCTGGAGTCTGACGGAGTATGGTTCTTCACGGTCCTCCCCAGGCAAGCACGGAGA
CCGTTTCATCCCGTCCCGAAGCGCAGCCAACTGGGACCTGAAATTCCATAGGACGCAAGACTCTGAGAAATCCCTGAAGG
AGAAGTGGCCATCCAGACAGGCCACATCGGGCAACAGCCCAATCTACTCTGCCTTGCTGGATAATGAGCTGCTGGGGGTC
GGCATTGAGAGAGTCCAGAATGTCAAGGGGAGGGGGCAAAGGCTTCCCCAGCCTTGCAGCCCAGAGAAGGAGGATCTCTT
TGTGTATAGCCCTAGCACTGAGGGCTGGTGGAGACCTGACGCGGTCCGTGCAGCCTCCTCTCATGGCATGTCATCCATCA
GCAGCAAAAGCCAGGCCTTACTGGCGTCGCAAAAGAAGACCCCGAAGAGCATCTCCGCAAAGCCTTTCAAAATCCTCGAG
GCCCCGGAGCTGCAAGACAACTTCTGCCTGAACCTACTAGACTGGTCTTCCCTCAACATCATCTCTGTGGGCCTGGGTAC
TTCTGTTTTCCTATGGCATGCCGCCACATGCCAGGTGGTGAGGGTATGTGACCTGTCAGTGGAGGGAGATTCCGTGACCT
CGGTGTGCTGGTCTCAGCGGGGCATTTTGCTAGCCGTGGGCACGCAGAAAGGGTTTGTGCATGTCTGGGACGTTGTAGCC
GAGAGGCGAGTGTGCGTGCTGAACAAGCACAGCTCCAGAGTCAGCGTGCTGGCCTGGAATGCCGACCAGATTTCTTCTGG
GAGCCGTGACAAGCTGATCCTCCAGAGGGACCTCCGCACCCGGGCCATGCAGTCTCGGCGCTGCCTCCAAGGCCACAGCG
GTGAGGTGTGTGGGCTCGAGTGGTCCACGAACCGCAGGCTGCTGGCCTCCAGCGGCAAGGACAATACGGTCGTGCTCTGG
ACGCCGGCCAGTCCAAAGCCTGTCCAGCAGCACACTGGCCACAAGGCGGCCGTGAAGGCCATCGCCTGGTCTCCCCATCA
GCATGGCCTCCTAGCGTCTGGTGGCTGCCAGGCCGACTGCGCCATCCTTTTCTGGAACACGCTGACCAATCAGATCCTCC
AGAGCATCCATACAGGTTCTCAGGTGGGCAACCTGGCCTGGTCCAGACACACCAACGAGCTGGTGAGCACCCACGGCTCC
CCGGAAAACCAGATCGCCATCTGGAAATACCCCTCCCTGGCACAAGCCAACAAGCTCACGGGCCACACCTGCCCAGTCTC
GCATCTGACCGTGTCTCCCGATGGACAGGTCATAGCTACAGGGGCTGCGGATGAGACTCTCAGACTCTGGGAAGTTTTTA
ACAAAACCCATCCGTCCAGACCATCCGAGTCCACCCTCGACCTCTTCACCCGTATCCGGTAA

Alignment

ORF - retro_mdom_296 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 95.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEMRRTLTPSNSPMSSPSKHGDRFIPSRAGANWSINFHRINENEKSPSQNRKAKDATSDNGKDGLAYSAL
          A.M...LT...S..SSP.KHGDRFIPSR..ANW...FHR....EKS.........ATS.N......YSAL
Retrocopy AKMSWSLTEYGSSRSSPGKHGDRFIPSRSAANWDLKFHRTQDSEKSLKEKWPSRQATSGNSP---IYSAL

Parental  LKNELLGAGIEKVQDPQTEDRRL-QPSTPEKKSLFTYSLSTKRS-SPDDGNEVSPYSLSPVSNKSQKLLR
          L.NELLG.GIE.VQ.......RL.QP..PEK..LF.YS.ST.....PD.....S....S..S.KSQ.LL.
Retrocopy LDNELLGVGIERVQNVKGRGQRLPQPCSPEKEDLFVYSPSTEGWWRPDAVRAASSHGMSSISSKSQALLA

Parental  SPRKPTRKISKIPFKVLDAPELQDDFYLNLVDWSSLNVLSVGLGTCVYLWSACTSQVTRLCDLSVEGDSV
          S..K....IS..PFK.L.APELQD.F.LNL.DWSSLN..SVGLGT.V.LW.A.T.QV.R.CDLSVEGDSV
Retrocopy SQKKTPKSISAKPFKILEAPELQDNFCLNLLDWSSLNIISVGLGTSVFLWHAATCQVVRVCDLSVEGDSV

Parental  TSVGWSERGNLVAVGTHKGFVQIWDAAAGKKLSMLEGHTARVGALAWNADQLSSGSRDRMILQRDIRTPP
          TSV.WS.RG.L.AVGT.KGFV..WD..A......L..H..RV..LAWNADQ.SSGSRD..ILQRD.RT..
Retrocopy TSVCWSQRGILLAVGTQKGFVHVWDVVAERRVCVLNKHSSRVSVLAWNADQISSGSRDKLILQRDLRTRA

Parental  VQTERRLQGHRQEVCGLKWSTDHQLLASGGNDNKLLVWNHSSLSPVQQYTEHLAAVKAIAWSPHQHGLLA
          .Q..R.LQGH..EVCGL.WST...LLAS.G.DN....W...S..PVQQ.T.H.AAVKAIAWSPHQHGLLA
Retrocopy MQSRRCLQGHSGEVCGLEWSTNRRLLASSGKDNTVVLWTPASPKPVQQHTGHKAAVKAIAWSPHQHGLLA

Parental  SGGGTADRCIRFWNTLTGQPLQCIDTGSQVCNLAWSKHANELVSTHGYSQNQILVWKYPSLTQVAKLTGH
          SGG..AD..I.FWNTLT.Q.LQ.I.TGSQV.NLAWS.H.NELVSTHG...NQI..WKYPSL.Q..KLTGH
Retrocopy SGGCQADCAILFWNTLTNQILQSIHTGSQVGNLAWSRHTNELVSTHGSPENQIAIWKYPSLAQANKLTGH

Parental  SYRVLYLAMSPDGEAIVTGAGDETLRFWNVFSKTRSTKESVSVLNLFTRIR
          ...V..L..SPDG..I.TGA.DETLR.W.VF.KT.....S.S.L.LFTRIR
Retrocopy TCPVSHLTVSPDGQVIATGAADETLRLWEVFNKTHPSRPSESTLDLFTRIR

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_296 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_296 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006919	4 retrocopies	retro_mdom_235, retro_mdom_270, retro_mdom_296 , retro_mdom_46,