RetrogeneDB ID: retro_mdom_567

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:325331689..325332202(-)
• Located in intron of: ENSMODG00000012835

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNDIG1L
• Ensembl ID: ENSMODG00000024016
• Aliases: None
• Description: synapse differentiation inducing 1-like [Source:HGNC Symbol;Acc:32388]

Sequence

>retro_mdom_567
ATGCAACTAGCTATAGAGGCACTGTATGAGTCCATCTTTCCCCCTGATGAAGGACAAAGCAAAAGAGTGTAAAGGTGATA
ACCATGGAACTAACTTCACAGAGAGCAAGGAGCTCCAGGCCAGCACCACTGAAGGAGTCCAGAGACCCAGCTAGGCTGAG
GAAGATGCCATTATTCAGACAATATGCTTTGAAGTAGAAAAGGAGTTTCTAGAGTTGGAAGAAGATGATAATGATGAGAG
TGATTCTTTCAAAGCCAGTGAGAGTGAAGATGTTTTCCTTATCTACCACCCTGGGACCACCTTGGCCTCACCATCTTCTC
CATGCTTTCTGTTCCATGGCCCCTGGGCATTGCTGCCTTCTACTTTTTACAAAGGACAAGCAAGGCAATCTCCAAAGGGG
ACTTTTGCCTGGCCAGCATGACTTCCTGACAGGCCCTTTTCCTGGCCATCCTTTTCATCACCACTGGCACCCATGTCAAT
GTTGCAGTGGTGGTGGCACTGGTGACTTACTTG

Alignment

ORF - retro_mdom_567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 72.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQLAVEALYGS-NFLLVKDKAKEWKGDSCETTFTESKEPQASTPERVQRPGEAEEDAKIQTVSFEVEEEF
          .QLA.EALY.S..F.L.KDKAKE.KGD...T.FTESKE.QAST.E.VQRP..AEEDA.IQT..FEVE.EF
Retrocopy MQLAIEALYES>SFPLMKDKAKECKGDNHGTNFTESKELQASTTEGVQRPS*AEEDAIIQTICFEVEKEF

Parental  LEVEEEDDDESDSSSASESEDGFLT-LPPRDHLGLAIFSMLCCFWPLGIAAFYFSQRTSKAISKGDFHLA
          LE.EE.D.DESDS..ASESED.FL..LPP.DHLGL.IFSML...WPLGIAAFYF.QRTSKAISKGDF.LA
Retrocopy LELEEDDNDESDSFKASESEDVFLI<LPPWDHLGLTIFSMLSVPWPLGIAAFYFLQRTSKAISKGDFCLA

Parental  SMTSRRAFFLAILSITIGTGVYIAVVVALVAYL
          SMTS..A.FLAIL.IT.GT.V..AVVVALV.YL
Retrocopy SMTS*QALFLAILFITTGTHVNVAVVVALVTYL

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	50.42 RPM
SRP007412_cerebellum	0.00 RPM	17.63 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	6.68 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_567 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_567 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	ENSMODG00000024016	1 retrocopy	retro_mdom_567 ,