RetrogeneDB ID: retro_mdom_106

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:167259725..167260871(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005208
• Aliases: None
• Description: None

Sequence

>retro_mdom_106
ATGGCGGCCCTGGGCAGTGTCCGTGTGATAAGCCAATCACTGGTAGTGGGTCGGAGACCTGGAGCCTGGAGGGGCCTGAT
CACCACAGCTGCCACCCACTCTGCTCAGCCAAAGCATGGGGTGGGTGATGAGAAGGAGGGTAAGGTGATACCTGTCACTA
TGGTGCCCGGTGATGGTGTGGGGCCTGAGCTTATGGAGGCTGTCAGAAAAGTCTTTAAGGCAGCCCTGGTCCCTGTGGAG
TTTCAGGAGTATCATCTGAGTGGGATGGAGAACATGGCCACAGAAGAGAAACTGGAACAAGTGCTGAACTCCATAAGGAA
AAATAAGATCGCGATCATTGGAAAAATCCATACGCCAATGGATAACAACAAAGGCATCTTGTCTTATAATATGCAGATCA
AGCGGAAACTGGATCTGTTTGCTAACGTTGTTCCGGTCCAGAGCCTTTTGGGATATGAGACCCGACACAACAACCTGGAC
TTGGTGATCATCCGGGAGCAGACTGAGGGAGAATATAGTGCCCTGGAGCATGAAAGTGTCAAGGGGGTGATTGAATGTTT
GAAGATCATCACTAGTTACAAGTCCCGGCGAATTGCCAAGTTTGCCTTTGACTATGCCACCAAAAAGGGTCGAAAGAAGG
TCACAGCCGTGCATAAGGCCAATATTATGAAGCTGGCTGATGGGCTCTTCCTGAAGTGTTGTGAGGAGGTGGCTGAGCTA
TACCCCAAGATCAAGTTTGAGAACATAATCATAGACAACTGTTGTCTACAGTTGGTGAAAAATCCATACCAATTTGATGT
GCTCGTGATGCCCAGTCTCTATGGAAACATTGTTGACAACTTGGCAGCAGGACTGGTGGGGGGTGCTGGTGTGGTTCCTG
GTGAGAGCTACAGTGGTGAATACGCTGTTTTTGAAACAGGTGCAAAGCACCAGTATAGCCAGGCTGCGGGCAAGAACATT
GCCAACCCTACTGCCATGCTACTGTCTTCCAGCAATATGCTGAATTACCTCAACCTGAAAGATCACTCCAGCAAGATTGC
TGGGGCTGTGAAGGCAGTGATAAAAACTGGCAAAATTCGGACTGAGGATATGGGCGGCAAAAACACCACATCAGAATTCA
TCGATTCGATTATCAAACACCTGTAA

Alignment

ORF - retro_mdom_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.2 %
• Parental protein coverage: 98.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALTGTRVLSRALVVTPNLGTWRGLMTTAAVR-ATPRSAVDDVKVEGAFPVTMLPGDGVGPELMHAVKE
          MAAL...RV.S..LVV....G.WRGL.TTAA...A.P...V.D.K.....PVTM.PGDGVGPELM.AV..
Retrocopy MAALGSVRVISQSLVVGRRPGAWRGLITTAATHSAQPKHGVGDEKEGKVIPVTMVPGDGVGPELMEAVRK

Parental  VFKAASVPVEFQEHHLSEVQNMASEEKLEQVLSSMKENKVAIIGKIHTPMDTEYKGDLASYDMRLTRKLD
          VFKAA.VPVEFQE.HLS...NMA.EEKLEQVL.S...NK.AIIGKIHTPMD...KG.L.SY.M...RKLD
Retrocopy VFKAALVPVEFQEYHLSGMENMATEEKLEQVLNSIRKNKIAIIGKIHTPMDNN-KGIL-SYNMQIKRKLD

Parental  L-ANVVHVKSLPGY-TRHNNLDLVIIREQTEGEYSSLEHESARGVIECLKIVTRAKSQRIAKFAFDYATK
          L.ANVV.V.SL.GY.TRHNNLDLVIIREQTEGEYS.LEHES..GVIECLKI.T..KS.RIAKFAFDYATK
Retrocopy LFANVVPVQSLLGYETRHNNLDLVIIREQTEGEYSALEHESVKGVIECLKIITSYKSRRIAKFAFDYATK

Parental  KGRGKVTAVHKANIMKLGDGLFLQCCEEVAELYPKIKFETMIIDNCCMQLVQNPYQFDVLVMPNLYGNII
          KGR.KVTAVHKANIMKL.DGLFL.CCEEVAELYPKIKFE..IIDNCC.QLV.NPYQFDVLVMP.LYGNI.
Retrocopy KGRKKVTAVHKANIMKLADGLFLKCCEEVAELYPKIKFENIIIDNCCLQLVKNPYQFDVLVMPSLYGNIV

Parental  DNLAAGLVGGAGVVPGESYSAEYAVFETGARHPFAQAVGRNIANPTAMLLSSSNMLRHLNLEYHSNMIAE
          DNLAAGLVGGAGVVPGESYS.EYAVFETGA.H...QA.G.NIANPTAMLLSSSNML..LNL..HS..IA.
Retrocopy DNLAAGLVGGAGVVPGESYSGEYAVFETGAKHQYSQAAGKNIANPTAMLLSSSNMLNYLNLKDHSSKIAG

Parental  AVKKVIKMGKVRTRDMGGYSTTSDFIKSVISHL
          AVK.VIK.GK.RT.DMGG..TTS.FI.S.I.HL
Retrocopy AVKAVIKTGKIRTEDMGGKNTTSEFIDSIIKHL

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_106 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_106 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005208	1 retrocopy	retro_mdom_106 ,
Otolemur garnettii	ENSOGAG00000004684	1 retrocopy	retro_ogar_2890,
Sarcophilus harrisii	ENSSHAG00000017173	1 retrocopy	retro_shar_94,
Tupaia belangeri	ENSTBEG00000011579	2 retrocopies	retro_tbel_3404, retro_tbel_4122,