RetrogeneDB ID: retro_dord_615

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_4091:5127..5457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B230118H07Rik
• Ensembl ID: ENSDORG00000010963
• Aliases: None
• Description: RIKEN cDNA B230118H07 gene [Source:MGI Symbol;Acc:MGI:1915420]

Sequence

>retro_dord_615
CTCAGTTTAGAAGATGTGGACATAGATGAAGAGACTGATCCCCAAATGAGCAAGGACAGGATGCCGCTTCAGGAGAAGTG
GAACAGGAATTAAGCACGTATGTTCCTTCTTACACTCCTGTGGTCCGGCCTCCCATCAATGAAGAGAAGCTGAAGCTACA
GTAAAAAGGACCATGGAGCAAGTGGCAGAGATACTTGGAGATGAAGTCAGCCCTTCTCACTTGATGAAGAATTTGATTAT
GACAATGTGACTCCAACCCCCAAGTACACTCCTGAAGACCTAGACACCATCAAAGAACTGTTGAAGCAAGGGAGAAAGAA
CACCAACACA

Alignment

ORF - retro_dord_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSLEDVDIDEETDPQMSKDRMLLP-GEVEQELSTYVPSYVPVDRPPINEEKLK-PTVKRTMEQVSEILGD
          LSLEDVDIDEETDPQMSKDRM.L..GEVEQELSTYVPSY.PV.RPPINEEKLK..TVKRTMEQV.EILGD
Retrocopy LSLEDVDIDEETDPQMSKDRMPLQ<GEVEQELSTYVPSYTPVVRPPINEEKLK<ATVKRTMEQVAEILGD

Parental  EV-QPFSLDEEFDYDNVTLTPKYTPEDIDTIKELLKQGRKNTST
          EV.QPFSLDEEFDYDNVT.TPKYTPED.DTIKELLKQGRKNT.T
Retrocopy EV<QPFSLDEEFDYDNVTPTPKYTPEDLDTIKELLKQGRKNTNT

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_615 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000010963	2 retrocopies	retro_dord_388, retro_dord_615 ,
Homo sapiens	ENSG00000166352	1 retrocopy	retro_hsap_418,
Gorilla gorilla	ENSGGOG00000004773	1 retrocopy	retro_ggor_411,
Macropus eugenii	ENSMEUG00000003065	1 retrocopy	retro_meug_328,
Microcebus murinus	ENSMICG00000008620	1 retrocopy	retro_mmur_383,
Monodelphis domestica	ENSMODG00000019838	1 retrocopy	retro_mdom_1594,
Pongo abelii	ENSPPYG00000003347	1 retrocopy	retro_pabe_302,
Pan troglodytes	ENSPTRG00000003514	2 retrocopies	retro_ptro_2924, retro_ptro_320,
Tupaia belangeri	ENSTBEG00000004277	2 retrocopies	retro_tbel_2155, retro_tbel_2277,