RetrogeneDB ID: retro_dord_419

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_17515:12348..12805(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab18
• Ensembl ID: ENSDORG00000014338
• Aliases: None
• Description: RAB18, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:102790]

Sequence

>retro_dord_419
GGAAATAGAGCTAAACTTACAATATGGGATACCGCTGGTCAAGAGAGGTTTAGAATCTTAACTCCCAGCTACTATAGAGG
TGCACAGGGTGTTATATTAGTTTATGATGTCACAAGAAGAGACACTTTTGTTAAGCTGGATAATTGGTTAAATGAATTGG
AGACATACTGTACACGAAATGACATAGTAGACATGCTGGTTGGAAATAAAATTGACAAGGAAAATTGTGAAGTTGATAGA
AATGAGGGCCTGAAATTTGCAAGAAAGCATTCCATGTTATTTATAGAGGCAAATGCAAAAACCTGTGATGGTGTACAATG
TGCCTTTGAAGAACTTGTTGAGAAGATCATTCAGACACCTGGACTGGGAAAGTGAGAACCAAAGCAAGGGCATGAAGCTG
TCACACAGGGAAGAAAGTCACGGTGGAGGAGCCTGTGGTGGTAACTCTTCTGTGTTA

Alignment

ORF - retro_dord_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.56 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GNKAKLAIWKDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGN
          GN.AKL.IW.DTAGQERFR.LTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIV.MLVGN
Retrocopy GNRAKLTIW-DTAGQERFRILTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVDMLVGN

Parental  KIDKENREVDRNEGLKFARKHSMLFIE-SAKTCDGVQCAFEELVEKIIQTPGLW-SENQNKGMKLSHREE
          KIDKEN.EVDRNEGLKFARKHSMLFIE..AKTCDGVQCAFEELVEKIIQTPGL..SENQ.KGMKLSHREE
Retrocopy KIDKENCEVDRNEGLKFARKHSMLFIEANAKTCDGVQCAFEELVEKIIQTPGLG>SENQSKGMKLSHREE

Parental  SHGGGACGGYCSVL
          SHGGGACGG..SVL
Retrocopy SHGGGACGGNSSVL

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_419 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633, retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419 ,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744, retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,