RetrogeneDB ID: retro_mdom_232

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:298489183..298489549(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023944
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020362
• Aliases: None
• Description: None

Sequence

>retro_mdom_232
GTCCTGTTCTTCCTCAATGGCTGGTACAGTGCCACCTACTTCCTGACGGAGCTTTTCACGTTCCTGTACAAGGGTCTCCT
GCTACCGTATCCAAAAACCAATCTAGTTCTGGACCTGGTGATGTTCTTCCTTTACCTTGGAACTGAAATCGTCCGCATCC
ATTTCGGCAGGAAAGGGAACCTCTGCGTAAGGATGACACCCCTGGGGATTAGCTTGGCCTTGACCTTCCCTTCGGCTCTG
ATGGCTTTCTATTACTTCCTGTTTCAGACGTATGTTCTTCGCATCGAGGCTGTGATGACCATGCTCCTGCTCCCCTTCTA
CATCATACAGGTGATCCTCGAGGTGCTCACACTCGCCACCTTGTCC

Alignment

ORF - retro_mdom_232 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 55.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILFFLNGWYSATYFLLELFTFLYKGLLLPYPTANLILDLVMLFLYLGIEITRIFFGTKGNLCQRMMPLGI
          .LFFLNGWYSATYFL.ELFTFLYKGLLLPYP..NL.LDLVM.FLYLG.EI.RI.FG.KGNLC.RM.PLGI
Retrocopy VLFFLNGWYSATYFLTELFTFLYKGLLLPYPKTNLVLDLVMFFLYLGTEIVRIHFGRKGNLCVRMTPLGI

Parental  SLALTFPSAMMASYYLLLQTYVLRLEAVMGTILLLFCALEVILEVLTLSTFS
          SLALTFPSA.MA.YY.L.QTYVLR.EAVM...LL.F....VILEVLTL.T.S
Retrocopy SLALTFPSALMAFYYFLFQTYVLRIEAVMTMLLLPFYIIQVILEVLTLATLS

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_232 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_232 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016592	1 retrocopy	retro_amel_1255,
Bos taurus	ENSBTAG00000021517	1 retrocopy	retro_btau_1184,
Canis familiaris	ENSCAFG00000016171	4 retrocopies	retro_cfam_1342, retro_cfam_331, retro_cfam_332, retro_cfam_333,
Monodelphis domestica	ENSMODG00000020362	1 retrocopy	retro_mdom_232 ,
Mustela putorius furo	ENSMPUG00000014169	4 retrocopies	retro_mputfur_1341, retro_mputfur_1536, retro_mputfur_1537, retro_mputfur_1538,
Oryctolagus cuniculus	ENSOCUG00000001682	1 retrocopy	retro_ocun_799,