RetrogeneDB ID: retro_dord_540

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_29131:16590..17101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aimp1
• Ensembl ID: ENSDORG00000005018
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 [Source:MGI Symbol;Acc:MGI:102774]

Sequence

>retro_dord_540
AAACAGCAAGCCTTAGCAGGAAGTGCTGACTCTAAACCAATAGATGTGTCCCGTTTGGACCTTCGAATTGGTTGCATTCT
TACTGCCAAAAAACATCCAGATGCTGATTCTTTACATGTAGAAGAAGTAGATGTTGGAGAAACATCCTCAAGAACAGTTG
TCAGTGGCCTGGTGAATCATGTTCCTCTCGAACAGATAGATGCAAAATTGGATGGTGATTTTACTTTGTAGTCTCAAACC
TGCAAAGATACAAGAGGTATTATCTTAATCAATGGTGATGTGTGCCAGTTCACCTGAAGTTGAAATTTTGGCTCCTCCAA
ATGTATCTGTTCCTGGAGATAGAATTACTTTTGATGCTTTCCCTGGAGAGCCTGATAAGGAGCTGAACCCTAAAAAGAAG
ATTTGGGAGCAGATCCAGCCTGATCTTTACACTAATAATGAGTGTGTGGCCACCTACAAGGGGGCACCCTTTGAGGTGAA
AGGAAAGGATGTGTGTAGGGCTCAAACCATG

Alignment

ORF - retro_dord_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 54.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQQALAGSADSKPIDVSRL-LRIGCILAAKKHPDADSLYVEEVDVGETAPRTVVSGLVNHVPLEQMQNRM
          KQQALAGSADSKPIDVSRL.LRIGCIL.AKKHPDADSL.VEEVDVGET..RTVVSGLVNHVPLEQ.....
Retrocopy KQQALAGSADSKPIDVSRLDLRIGCILTAKKHPDADSLHVEEVDVGETSSRTVVSGLVNHVPLEQIDAKL

Parental  -VILL-CNLKPAKMRGVLSQAMVMCASSPEKVEILAPPNGSIPGDRITFDAFPGEPDKELNSKKKIWEQI
          ....L.C.LKPAK...VLS..MVMCASSPE.VEILAPPN.S.PGDRITFDAFPGEPDKELN.KKKIWEQI
Retrocopy >MVILLCSLKPAKIQEVLS*SMVMCASSPE-VEILAPPNVSVPGDRITFDAFPGEPDKELNPKKKIWEQI

Parental  QPDLYTNNECVATYKGASFELKGK-VCRAQTM
          QPDLYTNNECVATYKGA.FE.KGK.VCRAQTM
Retrocopy QPDLYTNNECVATYKGAPFEVKGKDVCRAQTM

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_540 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540 ,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,