RetrogeneDB ID: retro_dord_588

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_36776:4250..4559(+)
• 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_588
TCCTCTGGTTCTATGGAAATTAAGAAGAAACAGCAAGATATTCTTGGCTTCTTAGAAGCTAACAAAATTGGATTTGAAGA
GAAAGATATTGCAGCCAGTGAAGAGAAGTGGATGAGAGAAAATGTACCTGAAAACAGTCGACCAGCCACAGGGTGCCCCG
TGCTGCCTCAGATTTTCAATGACAGCCAGTACCGTGGGGACTATGCTACCTTCTTTGAAGCCTGAGAAAATAATTCAGTT
TGTGTCTTTTTAGGACTGACAGCTCCACCTGGTTCAAAGGAGGCAGACAGCCAGGTAAAGCTGCCGGCA

Alignment

ORF - retro_dord_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.05 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSSTDIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGHPLPPQIFNESQYRGDY
          SS.S..IKKKQQD.LGFLEANKIGFEEKDIAA.EE..KWMRENVPENSRPATG.P..PQIFN.SQYRGDY
Retrocopy SSGSMEIKKKQQDILGFLEANKIGFEEKDIAASEE--KWMRENVPENSRPATGCPVLPQIFNDSQYRGDY

Parental  DAFFEARENNAVYAFLGLTAPPGSKEAEAQAKQQA
          ..FFEA.ENN.V..FLGLTAPPGSKEA..Q.K..A
Retrocopy ATFFEA*ENNSVCVFLGLTAPPGSKEADSQVKLPA

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_588 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.

---

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,