RetrogeneDB ID: retro_mdom_57

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:8014257..8014962(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025397
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021442
• Aliases: None
• Description: None

Sequence

>retro_mdom_57
ATGAAGATTTGGGGGAGCCACAAGTTCTTTAAAAAGAGGGTCATGGTCGACCCGCCCACAGACCTCAAATTTAAAGGCCC
CTTCACAGATGTAGTCACTACCGATCTTAAACTTCGAAATCCATCAGACAGAAAAGTATGTTTCAAAGTGAAGACAACAG
CACCTTGTCGGTACTGTGTGAGGCCAAACAGTGGGATTATTGATCCAGGGTTGACTGTAACTGTTTCAGTAATGCTACAG
CCTTTTGACTATGAGCCAAATGAGAAGAGTAAACACAAGTTTATGGTACAGACGATTTTTGCTCCAACAAACACTTCAGA
TATGGACGCTGTGTGGAAAGAAGCAAAACCTAATGAACCGATGGATTCTAAATTGAGATGTATACTTGAAATGCCCACTG
AAAACGATAAATTGATTGATATGGAGGCTGCTAAACCTCATTCAAAAGCAGATGGGACCCTGATGAAACAGTATAGTAGT
CCTTCATTCAATGATACGGCAACAAAAAGACTAGTGGAAAAGTGTAAACGACTTCAAGGAGAAATGATGAAATTATCAGA
AGAAAATCGACACCTGAGGGATGAAGGTTTAAAGCTCAGAAAGGTATCACAGATGGAAAAACGAAGCTCAAACGTGATTC
CTTCACTTCTTGTGGTAATTGCAGCCATTTTCATTGGATACTTTTTAGGGAAATTCATCTTGTAG

Alignment

ORF - retro_mdom_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.37 %
• Parental protein coverage: 86.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVLDPPTDLKFKGPFTDVVTTNLKLRNPSDRKVCFKVKTTAPRRYCVRPNSGIIDPGLTVTVSVMLQPFD
          ...DPPTDLKFKGPFTDVVTT.LKLRNPSDRKVCFKVKTTAP.RYCVRPNSGIIDPGLTVTVSVMLQPFD
Retrocopy VMVDPPTDLKFKGPFTDVVTTDLKLRNPSDRKVCFKVKTTAPCRYCVRPNSGIIDPGLTVTVSVMLQPFD

Parental  YDPNEKSKHKFMVQTIFAPTNTSDMDAVWKEAKPDELMDSKLRCIFEMPTENDKLVDMEAPKTHLKADGT
          Y.PNEKSKHKFMVQTIFAPTNTSDMDAVWKEAKP.E.MDSKLRCI.EMPTENDKL.DMEA.K.H.KADGT
Retrocopy YEPNEKSKHKFMVQTIFAPTNTSDMDAVWKEAKPNEPMDSKLRCILEMPTENDKLIDMEAAKPHSKADGT

Parental  LIKQHSSLALNDSETKKLMEECKRLQGEMMKLSEENRHLRDEGLKLRKGS
          L.KQ.SS...ND..TK.L.E.CKRLQGEMMKLSEENRHLRDEGLKLRK.S
Retrocopy LMKQYSSPSFNDTATKRLVEKCKRLQGEMMKLSEENRHLRDEGLKLRKVS

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_57 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_57 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006042	2 retrocopies	retro_cpor_783, retro_cpor_931,
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57 ,
Mus musculus	ENSMUSG00000024091	1 retrocopy	retro_mmus_1774,
Pongo abelii	ENSPPYG00000009006	1 retrocopy	retro_pabe_1323,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266,