RetrogeneDB ID: retro_mdom_1907

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:66178076..66178868(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025562
• Aliases: None
• Description: None

Sequence

>retro_mdom_1907
ATGGCTTCTAAAGAGATGAAGGAAGGTCTCCAAGATAGGTTGACCTGCGCCATTTGTCAAGCCTCTCTCACAGACCCAGT
GACTGTGGATTGTGGACACAGGGTTTGCCAATCTTGTCTTGATGACTCCAGCCAAGCTTCAGTGTCTTTCTCCTGTCCTG
AATGCAGGAAAGTCTCCCAGTCAAGAGCTTTTAAACTAGCTGTGAGGAAAAGGAAACCTGCTTTTAACTGCAGACAGCCG
CAGAGGTCTGTGGGACCCAGCAAGTGTGAGAGACACCAGGAGGCTCAGATGCTGTTCTGTATGGACGATAAGACCTTACT
CTGTGTATCCTGTTCACAATCCCAAGAACATGAGGCTCACACCATCCAACCCATAGAAGCAGCTGCTGGGGACTACAGGA
AAAAGCTCCAGGAGAATATGAAGCTTGTACATGAAACTTCAAAAGATGTTCAGAAGTTGATACTAGAGGAGAAGAAGGTA
CCTCGGACATGGGCTGTCCTGTGCACAGAGCAAGGAGAAATGCCAAGAAAAATGATTCAGGAAAGATTGAAAGAGGTAAG
TGATTTCCTGAGTGATGAAGAGGAAGAAGACCACAGTCTAATGGAACTGGATGAGGAAGAGAATGAAATGTTTGAGCACT
TGAAGGAGCACGAAGCCCAGCAGGAAATCCAAAACAGAGAGAAAAAGATGATGAGCAACTTCCAACTGTCCCAACACAAG
AATGACCTAAGGGAAATGGTCACAGCACTGGAAGAAAAGTCTCAGATGCCAGATAAGGAACTGCTCCAGAAT

Alignment

ORF - retro_mdom_1907 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.88 %
• Parental protein coverage: 93.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKEMKEGLQDTFTCTICQASLTDPVTVDCGHRVCQSCLDDSSQASGSFSCPECRKVSQSRAFKLAMRR
          MASKEMKEGLQD..TC.ICQASLTDPVTVDCGHRVCQSCLDDSSQAS.SFSCPECRKVSQSRAFKLA.R.
Retrocopy MASKEMKEGLQDRLTCAICQASLTDPVTVDCGHRVCQSCLDDSSQASVSFSCPECRKVSQSRAFKLAVRK

Parental  RKYAFNRRRAQRSEVPSKCDRHLEAQTLFCMDDKTLLCVSCSQSQEHEAHTIQPIEAAAGYYRKKLQENM
          RK.AFN.R..QRS..PSKC.RH.EAQ.LFCMDDKTLLCVSCSQSQEHEAHTIQPIEAAAG.YRKKLQENM
Retrocopy RKPAFNCRQPQRSVGPSKCERHQEAQMLFCMDDKTLLCVSCSQSQEHEAHTIQPIEAAAGDYRKKLQENM

Parental  KLVRETLKDVQKLILEEKKVPRTWA----EQVEMPRKTFQEKFKEISDFLSDEEEEVHSLMELDEEENEM
          KLV.ET.KDVQKLILEEKKVPRTWA....EQ.EMPRK..QE..KE.SDFLSDEEEE.HSLMELDEEENEM
Retrocopy KLVHETSKDVQKLILEEKKVPRTWAVLCTEQGEMPRKMIQERLKEVSDFLSDEEEEDHSLMELDEEENEM

Parental  FEHLKEHEVQQEIQNREKKMMSNFQLSQHKNDLREMVIALEEKSQMPDKELLQD
          FEHLKEHE.QQEIQNREKKMMSNFQLSQHKNDLREMV.ALEEKSQMPDKELLQ.
Retrocopy FEHLKEHEAQQEIQNREKKMMSNFQLSQHKNDLREMVTALEEKSQMPDKELLQN

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_1907 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1907 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025562	4 retrocopies	retro_mdom_1117, retro_mdom_1546, retro_mdom_1907 , retro_mdom_498,