RetrogeneDB ID: retro_mdom_135

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:406018514..406019549(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023542
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002377
• Aliases: None
• Description: None

Sequence

>retro_mdom_135
GAGCTCTCCTCAGTGCCCTCTGTCAATGGAATCTTCTGCAAGATGCAGCTGCTGGACGGGGGCAGCTTCTGCGCCGAGTC
TTCCAGAGAGGTGGTGCAAGCAAATTGTGTTCACTGGAGAAAGAAGTTCTCATTTATGTGGAAAATGAGTGCGAGTGCTG
CTACAGGCATTCTGGATCCTTGCATCTACAGGGTCTCTGTGAGGAAGGAATTAAAAGGTGGAAAGGCTTATGCAAAGCTG
GGCTTTGCAGATCTAAACCTAGCAGAGTTTGCTGGATCAGGAAATACCACTCGTCGCTGTTCACTAGAAGGTTATGATAC
CAAAAATACAAGACAAGATAATTCTATTCTTAAGGTCTTGATAAGCATGCAGCTCATGTCTGGTGATCCGTGTTTTAAAA
CACCTCCATCCACATCTATGTATATACCGATTGCTGGTGAATCTGAATCTCTACATGAGGATCAGAAGGGTGGAGAGACT
CTCAAAATCCATCTTGGATTGTCAGATCTTTCGGCAAAGAGTGCTTCCGTTCCAGATGAACTTGGTGCCTGTGGACACTC
CAGAACATCAAGCTATGCAAGCCAGCAATCAAAAGTATCAGGTTATAGTACATGTCACTCCAGGTCATCTAGTTTCCTTG
ACCTCTGCCACAAGAGAAATGCTTCAGTGGGAAGTACATCAACAAGAATTGAAAGTATCCTGGAGCCAAGTGATGATACT
GAACCAAAAATTGATCTTAATCCTGATGTACCTATTAAACAAGATTCGGATGAATCATCAGAAAAACTCAACAGGCACCC
TGTGAAGCAAGATTCTGTGGAATCTCAACTAAAACGTGTTTATGCTACCAGAGTGGATGCAGATGATATTGTTGAAAAAA
TATTGCAAAGTCAAGACTTCAGCTTGGACTCCAGTGCAGAAGAAGAAGGACTGAGGCTCTTTGTGGGTCCAGGAGGGAGT
ACGTCTTTTGGCAGTCATCACCTTCCAAATAGAGTGGGATCTGGTGCATATGAGCAAGTCCTGATCAAACGCTAA

Alignment

ORF - retro_mdom_135 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.52 %
• Parental protein coverage: 94.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELSSVPFVNGILFCKMRLLDGGSFCAESSREVVQANCVHWRKKFSFMCKMSASAATGILDPCIYRVSVRK
          ELSSVP.VNGI.FCKM.LLDGGSFCAESSREVVQANCVHWRKKFSFM.KMSASAATGILDPCIYRVSVRK
Retrocopy ELSSVPSVNGI-FCKMQLLDGGSFCAESSREVVQANCVHWRKKFSFMWKMSASAATGILDPCIYRVSVRK

Parental  ELKGGKAYAKLGFADLNLAEFAGSGNTTRRCLLEGYDTKNTRQDNSILKVLISMQLMSGDPCFKTPPSTS
          ELKGGKAYAKLGFADLNLAEFAGSGNTTRRC.LEGYDTKNTRQDNSILKVLISMQLMSGDPCFKTPPSTS
Retrocopy ELKGGKAYAKLGFADLNLAEFAGSGNTTRRCSLEGYDTKNTRQDNSILKVLISMQLMSGDPCFKTPPSTS

Parental  MYIPIAGESESLHEDRKGGETLKIHLGLSDLSAKSASVPDELGACGHSRTSSYASQQSKVSGYSTCHSRS
          MYIPIAGESESLHED.KGGETLKIHLGLSDLSAKSASVPDELGACGHSRTSSYASQQSKVSGYSTCHSRS
Retrocopy MYIPIAGESESLHEDQKGGETLKIHLGLSDLSAKSASVPDELGACGHSRTSSYASQQSKVSGYSTCHSRS

Parental  SSFSDLCHKRNASVGSTSTGIESILEPSDDTEPKVDLNPDVPIKQDGDESSEKLNRHPVKQDSVESQLKR
          SSF.DLCHKRNASVGSTST.IESILEPSDDTEPK.DLNPDVPIKQD.DESSEKLNRHPVKQDSVESQLKR
Retrocopy SSFLDLCHKRNASVGSTSTRIESILEPSDDTEPKIDLNPDVPIKQDSDESSEKLNRHPVKQDSVESQLKR

Parental  VDATRVDADDIVEKILQSQDFSLDSSAEEEGLRLFVGPGGSTSFGSHHLPNRVGSGAYEQVVIKR
          V.ATRVDADDIVEKILQSQDFSLDSSAEEEGLRLFVGPGGSTSFGSHHLPNRVGSGAYEQV.IKR
Retrocopy VYATRVDADDIVEKILQSQDFSLDSSAEEEGLRLFVGPGGSTSFGSHHLPNRVGSGAYEQVLIKR

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_135 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_135 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	ENSMODG00000002377	1 retrocopy	retro_mdom_135 ,