RetrogeneDB ID: retro_dord_416

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1731:85590..85911(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem18
• Ensembl ID: ENSDORG00000001854
• Aliases: None
• Description: transmembrane protein 18 [Source:MGI Symbol;Acc:MGI:2387176]

Sequence

>retro_dord_416
CAGACAGACTGGACGGAACTCTGGCTCTTGGGGCTCCTGGTCTTCCACCTGCTGTACCTGCTCCTCACCTGCTTCTCCTC
TCAGAGGTACAAACCACAGATTGGCCATTTCCTGTGCCTCGTGGCGTCGGTCTACTGTGCTGAGGATATCAATGAATGGC
CGCAGGGCACTGGAGGTCGTTTTCAAAATACCAGTATTTTGACTGCAGGGGGACTTTTCGTTTCTATCGTGTTCTCAGCA
CCGCTGCTGTTCAACGCGATGGTCACTGTGATTATGTGGGTTCACCAGACTTCGCATGTGATGACTGACCTGAAGAACTT
G

Alignment

ORF - retro_dord_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 88.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTDWTEPWLVGLLVFHLLCLLLTCFSSQRYKLQIGHFLCLVALVYCAEYINE-VAAVHWRSFSKHQYFDS
          QTDWTE.WL.GLLVFHLL.LLLTCFSSQRYK.QIGHFLCLVA.VYCAE.INE..AA.HWRSFSK.QYFD.
Retrocopy QTDWTELWLLGLLVFHLLYLLLTCFSSQRYKPQIGHFLCLVASVYCAEDINE<MAAGHWRSFSKYQYFDC

Parental  R-GMFISLVFSAPLLLNAMVIVIMWVHKTLNVMTELKNL
          R.G.F.S.VFSAPLL.NAMV.VIMWVH.T..VMT.LKNL
Retrocopy R>GLFVSIVFSAPLLFNAMVTVIMWVHQTSHVMTDLKNL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_416 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000543	1 retrocopy	retro_chof_31,
Cavia porcellus	ENSCPOG00000012522	1 retrocopy	retro_cpor_1298,
Dipodomys ordii	ENSDORG00000001854	1 retrocopy	retro_dord_416 ,
Equus caballus	ENSECAG00000008640	1 retrocopy	retro_ecab_596,
Monodelphis domestica	ENSMODG00000014284	1 retrocopy	retro_mdom_790,