RetrogeneDB ID: retro_dord_188

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4874:235776..236230(+)
• Located in intron of: ENSDORG00000003646

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nudcd2
• Ensembl ID: ENSDORG00000014291
• Aliases: None
• Description: NudC domain containing 2 [Source:MGI Symbol;Acc:MGI:1277103]

Sequence

>retro_dord_188
ATGTGGGCCCCTTTCGAGGAGCGCAGCGGGGGTGGTGCCGTGCGGGACGCCGTGGGGCCAGTGGTACCAGACGCTGGAGG
AGGTGTTCATCGAGGTGCGGGTGCCGCTGGGCATGCGCGTGCAGGACGTCCAGTGCGGCCTGCAGAGCCGGCACGTGGCG
CTGGCCGTGGGCGGCCGCGAGATGCTCAAGGGCAAGCTCTTTGATTCCACTATAGCTGATGAAGGAACATGGACTTTGGA
GGTTAGAAAAAGGGTCCGCATTGTTCTTACAAAGACAAAGAGAGACGCAGCCAACTGTTGGACTTCCCTTCTAGAATCTG
AATACGCCGCTGATCCTTGGGTACAAGACCAAATGCAGAGAAAGCTCACATTAGAGAGGTTCCAAAAAGAAAGTCCTGGC
TTTGACTTCAGTGGAGCTGAAATCTCAGGAAACTACACAAAAGGTGGACCAGAT

Alignment

ORF - retro_dord_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.76 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAPFEERSG-VVPCGTPWGQWYQTLEEVFIEVRVPPGTRAQDVQCGLQSRHVALAVGGREILKGKLFDS
          M.APFEERSG.VVPCGTPWGQWYQTLEEVFIEVRVP.G.R.QDVQCGLQSRHVALAVGGRE.LKGKLFDS
Retrocopy MWAPFEERSG>VVPCGTPWGQWYQTLEEVFIEVRVPLGMRVQDVQCGLQSRHVALAVGGREMLKGKLFDS

Parental  TIADEGTFFLEDRKMVRIVLTKTKRDAANCWTSLLESEYAADPWVQDQMQRKLTLERFQKENPGFDFSGA
          TIADEGT..LE.RK.VRIVLTKTKRDAANCWTSLLESEYAADPWVQDQMQRKLTLERFQKE.PGFDFSGA
Retrocopy TIADEGTWTLEVRKRVRIVLTKTKRDAANCWTSLLESEYAADPWVQDQMQRKLTLERFQKESPGFDFSGA

Parental  EISGNYTKGGPD
          EISGNYTKGGPD
Retrocopy EISGNYTKGGPD

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_188 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005270	1 retrocopy	retro_amel_535,
Bos taurus	ENSBTAG00000014772	1 retrocopy	retro_btau_1735,
Callithrix jacchus	ENSCJAG00000015367	1 retrocopy	retro_cjac_2093,
Cavia porcellus	ENSCPOG00000000877	1 retrocopy	retro_cpor_936,
Dipodomys ordii	ENSDORG00000014291	1 retrocopy	retro_dord_188 ,
Macropus eugenii	ENSMEUG00000004802	1 retrocopy	retro_meug_1673,
Myotis lucifugus	ENSMLUG00000001670	1 retrocopy	retro_mluc_1154,
Monodelphis domestica	ENSMODG00000007641	2 retrocopies	retro_mdom_1058, retro_mdom_2016,
Ornithorhynchus anatinus	ENSOANG00000021414	1 retrocopy	retro_oana_122,
Oryctolagus cuniculus	ENSOCUG00000005783	1 retrocopy	retro_ocun_819,
Otolemur garnettii	ENSOGAG00000024929	3 retrocopies	retro_ogar_1486, retro_ogar_1696, retro_ogar_482,
Sarcophilus harrisii	ENSSHAG00000007551	1 retrocopy	retro_shar_559,
Ictidomys tridecemlineatus	ENSSTOG00000028665	1 retrocopy	retro_itri_1770,
Tupaia belangeri	ENSTBEG00000000307	1 retrocopy	retro_tbel_507,
Tarsius syrichta	ENSTSYG00000008090	1 retrocopy	retro_tsyr_1638,