RetrogeneDB ID: retro_mdom_1492

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:8235962..8236779(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010573
• Aliases: None
• Description: None

Sequence

>retro_mdom_1492
CAGCGATGGGGCGCGTGGATGAGCGGGCTGGCGAGGGAGCCGGCCCGGTCCGTGGGGACTGTGAGTTCTCGGGCAATTGG
CCAGCTACGAGCTCGCCCTGAAGCTGCAGCGGAGGCTGAGGCTGGAGCAGGAGGTCAAGGGCGTCCTGATCCGGCAGCAA
AACGGCTTCGACAGGGTGCCCGTGCCGGCCTGGCCCTGCAGTTCCCCGAGCCCGGGAGACAAGCCACCCGCCAAGGAGCT
CACGGCCAACCCGGGCTCCGAGCTCAAGGAGCAGCTGAACGGCGTCAGGGCATCCACGAGGGAACGGCGCAGCCCCGGCC
CATCAAGGTCTTCAAGCCCTACACCGAGTTTCGCGAGTTCAGCTGCCGCCAGATCAAGGACATGGAGAGCCTCTTCCGAC
GGTATGACTCTGGGAAGGATGGCTACATCGACCTGATGGAACTGAAGCTGATGATGGAGAAGCTGGGGGCCCCCCCAGAC
CCACCTGGGGCTAAAGGAAATGATCAGGGAGGTGGATGAGGACCTCGACAGCAAGCTCAGCTTTCGGGAGTTTTTGCTGA
TTTTCCGCAAAGCAGCCTCAGGGGAACTGGAGGAAGATGGTGGCTTGATGTCCCTGGCCAAGTTCTCCGAGATCGACGTG
GCCATGGAAGGTGTGAAAGGAGCCAAGAATTTCTTTGAAGCCAAGGTCCATGCCCTGTCCGTGACCAGCCGGTTTGAAGC
TGAGATCAAAGTAGAGCAGAATGCCCGAAAGCAGGAGGAGGAGGACAGAAAACACCGGAGGGCTCTCTTCAGAGAACGCC
AAGCCACCTTCTCCCAG

Alignment

ORF - retro_mdom_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QRSGGWTSGLAREPAPSVGTVCPRA-MASYELALKLQRRLRLEQEAEDVPIPQQNGFDGVPAPAWPCGSP
          QR.G.W.SGLAREPA.SVGTV..RA..ASYELA...............V.I.QQNGFD.VP.PAWPC.SP
Retrocopy QRWGAWMSGLAREPARSVGTVSSRA>LASYELAXXXXXXXXXXXXXKGVLIRQQNGFDRVPVPAWPCSSP

Parental  SPGDEPPAKELTANAGSELKEQLN-RRQGIHEGTARPRPIKVFKPYTEFREFSRRQIKDMESLFRRYDSG
          SPGD.PPAKELTAN.GSELKEQLN.RRQGIHEGTA.PRPIKVFKPYTEFREFS.RQIKDMESLFRRYDSG
Retrocopy SPGDKPPAKELTANPGSELKEQLN<RRQGIHEGTAQPRPIKVFKPYTEFREFSCRQIKDMESLFRRYDSG

Parental  KDGYIDLMELKLMMEKLGA-PQTHLGLKEMIREVDEDLDSKLSFREFLLIFRKAASGELEEDSGLMSLAK
          KDGYIDLMELKLMMEKLGA.PQTHLGLKEMIREVDEDLDSKLSFREFLLIFRKAASGELEED.GLMSLAK
Retrocopy KDGYIDLMELKLMMEKLGA>PQTHLGLKEMIREVDEDLDSKLSFREFLLIFRKAASGELEEDGGLMSLAK

Parental  LSEIDVAMEGVKGAKNFFEAKVHALSVTSRFEAEIKAEQNARKQEEEDRKHRRALFRERQAAFSQ
          .SEIDVAMEGVKGAKNFFEAKVHALSVTSRFEAEIK.EQNARKQEEEDRKHRRALFRERQA.FSQ
Retrocopy FSEIDVAMEGVKGAKNFFEAKVHALSVTSRFEAEIKVEQNARKQEEEDRKHRRALFRERQATFSQ

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_1492 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1492 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003684	1 retrocopy	retro_chof_1298,
Equus caballus	ENSECAG00000024045	1 retrocopy	retro_ecab_85,
Macropus eugenii	ENSMEUG00000008640	1 retrocopy	retro_meug_1315,
Monodelphis domestica	ENSMODG00000010573	2 retrocopies	retro_mdom_1492 , retro_mdom_211,