RetrogeneDB ID: retro_mdom_1546

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:193937988..193938810(-)
• 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_1546
ATGGCTTCTAAAGAGATGAAGGAAGGTCTCCAAGATATGTTTACCTGCACCATTTGTCAAGCCTCTCTCACAGACCCAGT
GACTGTGGATTGTGGACACAGGGTTTGCCAAACTTGTCTTGATGGCTCCAGACAAGTTTTGGGGTCTTTCTCCTGCCCTG
AATGCATGAAAGTCTCCCAGTCAAGAGCTTTTAAACTAGCTATGAGGAGAAGGAAACCTGCTTTTAACTGCAGACAGCTG
CAGAGGTCTGAGGGACCCAGCAAGCCTGACAGACACCTGGAAGCTCAGACGATGTTCTGTATGGATGATAAGACCTTACT
CTGTGAGTCCTTTTCACAATCCCAGGAACATGAGGCTCACATGATCCAACCCATAGAAGCAGCTGCTGGGGACTACAGGA
AAAAGCTCCAGGAGAATATGAAACTTGTATGTGAAACTTTAAAAGATGTTCAGAAGTTGATACTAGAGGAGAAGAAGGTA
CCTCAGACATGGGCTGTCCTGTGGACAGAACAAGTAGAAATGCCAAGAAAAATGTTTCAGGAAAAATTTAAAGAAATAAG
TGATTTCCTGAGTGATGAAGAGGAAGAAGTCCCCATTATAATGGAACTGGATGAGGAGGAGAATGAAATGTTTGTGCACT
TGAAGGAGCATGAGGCCCAGCGAGAAATCCAAAACAGAGAGAAAAAGATGATGAGCAACTTCCAACTGTCCCAACACAAG
AATGACCTATGGGAAATGGTCACAGCACTGGAAGAAAAGTCTCAGATGCCAGATAAGGAACTGCTCCAGGATGCAGGAAA
TACACTGAGCAAGAGTGAGACA

Alignment

ORF - retro_mdom_1546 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.23 %
• Parental protein coverage: 97.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKEMKEGLQDTFTCTICQASLTDPVTVDCGHRVCQSCLDDSSQASGSFSCPECRKVSQSRAFKLAMRR
          MASKEMKEGLQD.FTCTICQASLTDPVTVDCGHRVCQ.CLD.S.Q..GSFSCPEC.KVSQSRAFKLAMRR
Retrocopy MASKEMKEGLQDMFTCTICQASLTDPVTVDCGHRVCQTCLDGSRQVLGSFSCPECMKVSQSRAFKLAMRR

Parental  RKYAFNRRRAQRSEVPSKCDRHLEAQTLFCMDDKTLLCVSCSQSQEHEAHTIQPIEAAAGYYRKKLQENM
          RK.AFN.R..QRSE.PSK.DRHLEAQT.FCMDDKTLLC.S.SQSQEHEAH.IQPIEAAAG.YRKKLQENM
Retrocopy RKPAFNCRQLQRSEGPSKPDRHLEAQTMFCMDDKTLLCESFSQSQEHEAHMIQPIEAAAGDYRKKLQENM

Parental  KLVRETLKDVQKLILEEKKVPRTWA----EQVEMPRKTFQEKFKEISDFLSDEEEEVHSLMELDEEENEM
          KLV.ETLKDVQKLILEEKKVP.TWA....EQVEMPRK.FQEKFKEISDFLSDEEEEV...MELDEEENEM
Retrocopy KLVCETLKDVQKLILEEKKVPQTWAVLWTEQVEMPRKMFQEKFKEISDFLSDEEEEVPIIMELDEEENEM

Parental  FEHLKEHEVQQEIQNREKKMMSNFQLSQHKNDLREMVIALEEKSQMPDKELLQDAGNTLSKIST
          F.HLKEHE.Q.EIQNREKKMMSNFQLSQHKNDL.EMV.ALEEKSQMPDKELLQDAGNTLSK..T
Retrocopy FVHLKEHEAQREIQNREKKMMSNFQLSQHKNDLWEMVTALEEKSQMPDKELLQDAGNTLSKSET

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_1546 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1546 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,