RetrogeneDB ID: retro_mdom_1891

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:266240789..266241882(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010854
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014087
• Aliases: None
• Description: None

Sequence

>retro_mdom_1891
TCTCATCTGCAAAAAGTGAAGGAAGCTGATAAGAATGTAAAAGCTGGTGAGGAGCCTCCTGACAAAAAAGCCACCCAAAA
CTGTGAGAAAAAGCGGAAAGGAGAAAAGAGAAAGCCTGAACCAGGATGGTTTCATGTTGAAGAGGACAGCAACACAAATG
TATATGTTACTGGCTTACCTCCAGACATTACAAAGGATGAATTTGTACAACTTATGTCCAAATGTGGCATTATCATGAAA
GACCCCCCAAACAGATGAATGTAAAATCAAGCTTTATAAAGATAAACAAGGAAATCTTAAAGGAGATGGGGTTTGCTGTT
ATTTGAAGAAAGAATCGGTTGATCTAGCATTAAAGCTTCTAGATGATGATGTAATCAGAGGTTACAAACTGCATGTGGAA
AAGGCTAAGTTTCAGCTCAAGGGTGAATATGATGACAGGAAAAAGAAGAAGAAATGCAAAGACTACAGGAAAAAGCTGTC
TCTACAACAAAAACAGCTAGATTGGAGGCCTGAGAAAAAAGCTGGTTCAATGAGAATGCGACATGAGAGGGTTGTCATTA
TTAGGAATATGTTCCATCCAAAGGATTTTGAGGAGGATCCATTAGTGCTAAATGAAATCAGAGAAGACCTCCAAACAGAG
TGTGAGAAGTTTGGGCAAGTAAAGAAGGTCCTTCTCTTTGATAGACACCCAGATGGTGTGGCCTCTGTGTCCTATAAGGA
ACCAGAAGAAGCTGATCTCTGCATACAAGCCCTCAATGGAAGGTGGTTTGGTGGTCGCCAGTTGCATGTGGAAGTATGGG
ATGGTGTGACAGATTATCAGGTGGAGGAGACATCAAGAGAGAGAGAAGAACAACTGAAAGGCTGGGATAATTTTTTAGAG
AATCCTATCACCCAGAAAGAAACCCATTCATTTGATCCTGATTCTGCTTCTGGAAGCATGACCCGGGTATAGGGAAAACA
GTCCCCAGAAAATGGTACACCAAAAGAGCAAACCAAGGAGGAAGTGAATAATGGAGAAAGCTTCATTGAAGATGGGGCCC
TGTCTACAGACCGCAGCCTTGGAGGCAGTGATAATGAAGACACAGAACATCTT

Alignment

ORF - retro_mdom_1891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 80.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHPQKAKESDKNVKAGEDPTDQKTAQNSEKKQKGEKRKPEPGWFHVEEGRNTNVYVTGLPPDITKDEFIQ
          SH.QK.KE.DKNVKAGE.P.D.................PEPGWFHVEE..NTNVYVTGLPPDITKDEF.Q
Retrocopy SHLQKVKEADKNVKAGEEPPDXXXXXXXXXXXXXXXXXPEPGWFHVEEDSNTNVYVTGLPPDITKDEFVQ

Parental  LMSKCGIIMKDP-QTEEYKIKLYKDKQGNLKGDGLCCYLKKESVDLALKLLDDDVIRGYKLHVEKAKFQL
          LMSKCGIIMKDP.QT.E.KIKLYKDKQGNLKGDG.CCYLKKESVDLALKLLDDDVIRGYKLHVEKAKFQL
Retrocopy LMSKCGIIMKDP>QTDECKIKLYKDKQGNLKGDGVCCYLKKESVDLALKLLDDDVIRGYKLHVEKAKFQL

Parental  KGEYDASKKKKKCKDYRKKLSLQQKQLDWRPEKKAGSTRMRHERVVVIRNMFHPKDFEEDPLVLNEIRED
          KGEYD..KKKKKCKDYRKKLSLQQKQLDWRPEKKAGS.RMRHERVV.IRNMFHPKDFEEDPLVLNEIRED
Retrocopy KGEYDDRKKKKKCKDYRKKLSLQQKQLDWRPEKKAGSMRMRHERVVIIRNMFHPKDFEEDPLVLNEIRED

Parental  LRTECEKFGQVKKVLLFDRHPDGVASVSYKEPEEADLCIQALNGRWFGGRQLHVEVWDGVTDYQVEETSR
          L.TECEKFGQVKKVLLFDRHPDGVASVSYKEPEEADLCIQALNGRWFGGRQLHVEVWDGVTDYQVEETSR
Retrocopy LQTECEKFGQVKKVLLFDRHPDGVASVSYKEPEEADLCIQALNGRWFGGRQLHVEVWDGVTDYQVEETSR

Parental  EREERLKGWESFLENPNTQKETHLFDPDSASGSMPLTAGKQSPENNAPKGPTKEEVNNGESFNEDEAQST
          EREE.LKGW..FLENP.TQKETH.FDPDSASGSM....GKQSPEN..PK..TKEEVNNGESF.ED.A.ST
Retrocopy EREEQLKGWDNFLENPITQKETHSFDPDSASGSMTRV*GKQSPENGTPKEQTKEEVNNGESFIEDGALST

Parental  DSSLGDSDNEDTGHL
          D.SLG.SDNEDT.HL
Retrocopy DRSLGGSDNEDTEHL

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_1891 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1891 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009234	1 retrocopy	retro_mluc_352,
Monodelphis domestica	ENSMODG00000014087	3 retrocopies	retro_mdom_1255, retro_mdom_1891 , retro_mdom_193,