RetrogeneDB ID: retro_mdom_1849

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:95425327..95426046(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003806
• Aliases: None
• Description: None

Sequence

>retro_mdom_1849
TATCTTCTGGGCAAAGAGGAGATGACTAACAAGTTCTGCTGCTTTACTCTGGATCTGCTCAAAGTCCTAGGCAAAAGCAA
GTAACCGTTTTGATAGGTGGCCAAAGTGTTTCCTATACCATAGTTTGCAGGCTTCCAGGCATACTACCAGGATGAAGATG
GGGACCTAATTGTCTTTTTAAGTGAAGAAAGAGACAGGTCATGTGCTACATTAAAGAAGAGATCTTTAGGATTTGCATTA
AGGAGAAGAAGGAATGAAAGTGGAAGCTTCAGCACCCTTTAGTCCAGGAAGTTGCCACAAACATGGTACAGACCAACATG
ATCTATGATGGCTGCAATGGATCAATGATAGGAGATCACTTCAAATGTACCATCTGTCTTGATTATGACCTCTTTAGCAC
CTGTGAGGGCAAAAGGCTTCACAAAGAACTTAACATGATCAACTTTTGTAATCTCTTCAACCACCTTCCTGAGTGGATTT
CCCACCAAAGTTGGTTTCAAAATTTAAAACATAGGTCTTTCCCTGCTTTTGGTGTGTGAATGCCATGCTACTGGGGATTC
TTTCCTGCTGATCACATGAAACAAAATGCATCACAGGCACAAATGAATAGGACTTTACCTAACTGAGGAGAACAAGATAG
TCCCAGTTCACAACAGGACCCCAATGTCACCTTTCTGCAGAATGTAGGTAAAATTGTGGCAGCTCGCATTGCCCCTGTG

Alignment

ORF - retro_mdom_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLMGKEETAREIRRFTLDPVDGPGRCEQLLRRVAEVFPALRPGGFQAYYRDEDGDLIAFSSDEELGMAMC
          YL.GKEE.......FTLD.....G........VA.VFP.....GFQAYY.DEDGDLI.F.S.EE......
Retrocopy YLLGKEEMTNKFCCFTLDLLKVLGKSK*PF**VAKVFPIP*FAGFQAYYQDEDGDLIVFLS-EERDRSCA

Parental  YIKEDILRIYVKEKK-ECKREHRPPCVQEVPTNMVHPNVICDGCNGPVVGNRFKCTICPDYDLCNACEAK
          ..K...L.........E.K.....P.VQEV.TNMV..N.I.DGCNG...G..FKCTIC.DYDL...CE.K
Retrocopy TLKKRSLGFALRRRR<E*KWKLQHPLVQEVATNMVQTNMIYDGCNGSMIGDHFKCTICLDYDLFSTCEGK

Parental  GLHKEHNMILFQNPFNH-PEWISRRRWLQKMRHGPNFPAFGGWMPGCWGFFPPDALNQIAAQAQTNRTPP
          .LHKE.NMI.F.N.FNH.PEWIS...W.Q...H...FPAFG..MP..WGFFP.D...Q.A.QAQ.NRT.P
Retrocopy RLHKELNMINFCNLFNHLPEWISHQSWFQNLKH-RSFPAFGV*MPCYWGFFPADHMKQNASQAQMNRTLP

Parental  NTGAEQASTSSQQDPNVTFLQNVGESVAAALSPL
          N.G.EQ.S.SSQQDPNVTFLQNVG..VAA...P.
Retrocopy N*G-EQDSPSSQQDPNVTFLQNVGKIVAARIAPV

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	913.64 RPM
SRP007412_cerebellum	0.00 RPM	1111.58 RPM
SRP007412_heart	0.00 RPM	802.99 RPM
SRP007412_kidney	0.00 RPM	1135.11 RPM
SRP007412_liver	0.00 RPM	741.64 RPM
SRP007412_testis	0.00 RPM	686.93 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1849 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1849 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003806	1 retrocopy	retro_mdom_1849 ,
Nomascus leucogenys	ENSNLEG00000007969	1 retrocopy	retro_nleu_703,
Rattus norvegicus	ENSRNOG00000003147	1 retrocopy	retro_rnor_2916,