RetrogeneDB ID: retro_mdom_767

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:396205404..396206012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALX3
• Ensembl ID: ENSMODG00000001755
• Aliases: None
• Description: ALX homeobox 3 [Source:HGNC Symbol;Acc:449]

Sequence

>retro_mdom_767
GTCTCCAAAGTTACCAGTTTCACTCCATCACCTCTAGATTGTGCAGGAGGCCTCTTAGAAGGACCCCAAAGTTGACGGGC
TCTCCAGAATCTTGCCTGGGCAGACCCTGGGGACTTCTAAATCCCTAGCTCATTGACTCAATGGAACTGCCCAAAAGCAA
AAACAAGAAATAGAGGAACTGAGCTATACTCAGCACCTTCCAACAGGAAGGGATATATAAGGTTTTCCAGAAAACCCATT
ATTCTACATGTATACAAGGGAACAGTTAGCCTTCAGGACCAACCTGACTGAGGTCTGGATCAGGTCTGCTGCTAAAACTA
AAGAGCCAAGGAGAGGAGACGGGAAAGATATGGAAAGATCCAGGAAGGGAGGAATTCTTTCATGACCAACTATGATATTT
CAAATGTTTCCCAGAATAGATTGCTACACCCAGCTACAGAGCAACCTGTGGCCAAACCCAGGGTCAAGTTGCCCAGGAGG
GCCCTGTCTCATATTCCCAGGGGGGTCTGATTTCCATGCACCTCACCATACTCCCATTCCCACAGTGATGTGGCTAGTAT
TAGGGGCATGCCAACCTCCCCAGGACCTCCCCAGGCATTTATTCCATT

Alignment

ORF - retro_mdom_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.71 %
• Parental protein coverage: 60.71 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VSKVASFPPLPLDCPGGPLESPS-ELTGSPAPCLARLRGPLSPQLTDSMELPKSKNKKRRNRTTFSTFQL
          VSKV.SF.P.PLDC.GG.LE.P...LTGSP..CL.R..G.L.P.L.DSMELPKSKNKK.RN....STFQ.
Retrocopy VSKVTSFTPSPLDCAGGLLEGPQ<KLTGSPESCLGRPWGLLNP*LIDSMELPKSKNKK*RN*AILSTFQQ

Parental  EELEKVFQKTHYPD-VYAREQLALRTDLTEARV-QVWFQNRRAKWRKRERYGKIQEVRNPFTATYDIS-V
          E...KVFQKTHY....Y.REQLA.RT.LTE....QV...N.RAK.R.RERYGKIQE.RN.F...YDIS..
Retrocopy EGIYKVFQKTHYST<MYTREQLAFRTNLTEVWI<QVCC*N*RAKERRRERYGKIQEGRNSFMTNYDIS>M

Parental  LPRTDSYPQLQSNLWPSPGSGSPGGPCLM-SPEGIPSPCTSPYSHSHSNVAGFMGVPASPGPP-PGIYSI
          .PR.D.Y.QLQSNLWP.PGS..PGGPCL...P.G...PCTSPYSHSHS.VA...G.P.SPGPP.PGIYSI
Retrocopy FPRIDCYTQLQSNLWPNPGSSCPGGPCLI<IPRGV*FPCTSPYSHSHSDVASIRGMPTSPGPP<PGIYSI

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_767 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_767 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001755	1 retrocopy	retro_mdom_767 ,