RetrogeneDB ID: retro_mdom_1769

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:36328086..36328500(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012167
• Aliases: None
• Description: None

Sequence

>retro_mdom_1769
GCACTTGGCTTGCTGAAAATCCTGCAGAGGAGGAGGGTCTGAAAATTACCAGGGAATTTCTCTGTGACCAGAATAAGAAG
CATATTGATGAAGAAAATCTGGAGGAAAAACTCACTGTCTTCAAGAAGTATCTGGAATTTGACCTGAACAATGAAGGGAA
AAATTGACTTGATGTCCCTGAAGCAGATGATGGAGAAATTGGGTGTCCCAAAGACCCACCTGGTCATGAAGAAGATAATC
CCTGAAGTGATAGGTGGACTCACTGATACCATTTCCTAGCTGGACTTTCTGAATATGATGCTTGGAAAACGTTCAGCCAT
TCTCAAACTAGTCATGATGTTTGAAGGAAAAGACAGTAAAAGTTCCCCCAAGTCTGTTGGCCCCCCTCCTTAGAGAGACT
TTACCAGCCTTCCC

Alignment

ORF - retro_mdom_1769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 88.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AFGLLKARQGRRL-EEINREFLCDQ--KYSDEENLEEKLTAFKEKYMEFDLNNEGE-IDLMSLKRMMEKL
          A.GLLK..Q.RR....I.REFLCDQ..K..DEENLEEKLT.FK.KY.EFDLNNEG..IDLMSLK.MMEKL
Retrocopy ALGLLKILQRRRV<LKITREFLCDQNKKHIDEENLEEKLTVFK-KYLEFDLNNEGK>IDLMSLKQMMEKL

Parental  GVPKTHLEMKKIISEVTGGVSDTISYRDFVNMMLGKRSAVLKLVMMFEGKANESAPKPVGPPPERDIASL
          GVPKTHL.MKKII.EV.GG..DTIS..DF.NMMLGKRSA.LKLVMMFEGK...S.PK.VGPPP.RD..SL
Retrocopy GVPKTHLVMKKIIPEVIGGLTDTIS*LDFLNMMLGKRSAILKLVMMFEGKDSKSSPKSVGPPP*RDFTSL

Parental  P
          P
Retrocopy P

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	248.41 RPM
SRP007412_cerebellum	0.00 RPM	203.71 RPM
SRP007412_heart	0.00 RPM	14.95 RPM
SRP007412_kidney	0.00 RPM	1976.57 RPM
SRP007412_liver	0.00 RPM	2.52 RPM
SRP007412_testis	0.00 RPM	26.13 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1769 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1769 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012167	2 retrocopies	retro_mdom_1769 , retro_mdom_749,
Otolemur garnettii	ENSOGAG00000016759	2 retrocopies	retro_ogar_821, retro_ogar_93,
Tursiops truncatus	ENSTTRG00000003925	1 retrocopy	retro_ttru_959,