RetrogeneDB ID: retro_mdom_1761

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:14715596..14716398(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBC1D19
• Ensembl ID: ENSMODG00000000109
• Aliases: None
• Description: TBC1 domain family, member 19 [Source:HGNC Symbol;Acc:25624]

Sequence

>retro_mdom_1761
GTAAATCAATGTGGCTCAATGGCTTTTTTAAAAGAATTGTGGGTCATTATTTTGAATATTTCTAAACAAATTGAGATTTT
ATTGTATTATGAGAAACGCAAGTTCAATGTGATTCAACATGACCTTCTAGTGGATAGCATCATTTATGAGGATGTGAAGT
CGACAGCCAATAGTAATGATTGCCATTTTGTGTTTTGAACATTATTTGTCACAGATATTATTTTGTTCCCCTCAGGAAGT
ATGTGTATTAGGACACTTTGTTTAAAATTGTACTTTTTCTCCACTGAAGTCATATATAAAAGGAAAATTGGGAATGGAAG
ATTATGCTATCTTATCTACCAAAGGGTATAATCTCTTTAAATGGATTTTAATGTATGTTGCTCCCCTTTATGTTCATACC
ACAAGCATTCCAAATTGTATTATATAGTCCCTAAGAGCAATACACATTTTTTCTTCAGATTGCATTCCCTCTCTTCTCAT
CCCTCTTATATTGTTTCGCTCTTTGCTGTTTGAGATATCTCTTCAAACTCATCTTCCACAACTGTTTTTATTATCTAGAA
GAAATTGGAGCTCAGCCAATTTATATATCACTTAAGTGGAGTTGTACACACATTCTCCAGTTACCTAGCTACAGATCAGC
TTTTGCTTTTATGGAATAGAAACTGAGAATACAACTCTCTGGAAAATTCTTGCTGTTCTGGCAGCTGCCTTGTTTACTTT
CAGAACAGTAAACCCACCAGAAGTGACATCACTGACTGTGGCTGAAGCTGTGCTTGCTGATCTTTCCACTTTAAAAGTTA
TG

Alignment

ORF - retro_mdom_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.68 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IRQGSPTALRAELWALILNVSNQPEDLLYYEQLKSNVIQHDLLVDSLIYKDVKLTASNDDYYFV-FEDYL
          ..Q....A...ELW..ILN.S.Q.E.LLYYE..K.NVIQHDLLVDS.IY.DVK.TA...D..FV.FE.YL
Retrocopy VNQCGSMAFLKELWVIILNISKQIEILLYYEKRKFNVIQHDLLVDSIIYEDVKSTANSNDCHFV>FEHYL

Parental  YQVLLCFSRDTAVLGHFAYN-SASPPKSYIRGKLGMEDYAV-FYPPNGVIPFHGF-SMYVAPL-CFLYHE
          .Q.L.C......VLGHF..N...SP.KSYI.GKLGMEDYA....P..G.I...GF..MYVAPL....YH.
Retrocopy SQILFCSPQEVCVLGHFV*NCTFSPLKSYIKGKLGMEDYAI>YLP-KGIISLNGF<LMYVAPL<LCSYHK

Parental  PSKLYQIFREMYVRFFFRLHSISSHHSGIVSLCLLFETLLQTHLPQLFYHLREIGAQPLRISFKWMVRAF
          .SKLY.I.......FFFRLHS.SSH.S.IVSL...............F..................V..F
Retrocopy HSKLYYIVPKSNTHFFFRLHSLSSHPSYIVSLFAV*DISSNSSSTTVFII*KKLELSQFIYHLSGVVHTF

Parental  SGYLATDQLLLLWDRILGYNSLE-ILAVLAAAVFAFRAVNLMEVTSLAAAEAVLADLSTLKVM
          S.YLATDQLLLLW.R...YNSLE.ILAVLAAA.F.FR.VN..EVTSL..AEAVLADLSTLKVM
Retrocopy SSYLATDQLLLLWNRN*EYNSLE>ILAVLAAALFTFRTVNPPEVTSLTVAEAVLADLSTLKVM

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_1761 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1761 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
Loxodonta africana	ENSLAFG00000009636	1 retrocopy	retro_lafr_162,
Monodelphis domestica	ENSMODG00000000109	1 retrocopy	retro_mdom_1761 ,