RetrogeneDB ID: retro_dord_199

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5236:35848..36159(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sh3bgrl
• Ensembl ID: ENSDORG00000011106
• Aliases: None
• Description: SH3-binding domain glutamic acid-rich protein like [Source:MGI Symbol;Acc:MGI:1930849]

Sequence

>retro_dord_199
TCCGGCTCTATGGTGATTAAGAAGAAACAACAAGATGTGCTTGGCTTCTTAGAAGCCAACAAAATTGGATTTGAAGAGAA
AGATATTGCAGCCAATGAAGAGAACAGGAAGTGGATGAGAGAAAATGTACCTGAAAACAGTCGACCAGCCACAGGGCACC
CCTGCCACCTCAGATTTTCAATGAAAGCCAGTACCGTGGGGACTATAATGCCTTCTTCGAAGCCTGAGAAAATAATGCAG
TGTATGCCTTTTTAGGATTGACAGCTCCACCTGGCTCAATGGAGGCAGAAGCCCAGGCGAAGCAGCAAGCA

Alignment

ORF - retro_dord_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSTDIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGHP-LPPQIFNESQYRGDY
          S.S..IKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGHP.LPPQIFNESQYRGDY
Retrocopy SGSMVIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGHP<LPPQIFNESQYRGDY

Parental  DAFFEARENNAVYAFLGLTAPPGSKEAEAQAKQQA
          .AFFEA.ENNAVYAFLGLTAPPGS.EAEAQAKQQA
Retrocopy NAFFEA*ENNAVYAFLGLTAPPGSMEAEAQAKQQA

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_199 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004130	1 retrocopy	retro_chof_647,
Callithrix jacchus	ENSCJAG00000003568	2 retrocopies	retro_cjac_1102, retro_cjac_140,
Dipodomys ordii	ENSDORG00000011106	2 retrocopies	retro_dord_199 , retro_dord_588,
Equus caballus	ENSECAG00000012612	1 retrocopy	retro_ecab_648,