RetrogeneDB ID: retro_dord_577

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_35254:5697..6218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Npm3
• Ensembl ID: ENSDORG00000003491
• Aliases: None
• Description: nucleoplasmin 3 [Source:MGI Symbol;Acc:MGI:894653]

Sequence

>retro_dord_577
ATGGCCGATAGTGCTGCTGCTAATTTACCATTCCTGAGCCAGGGAAGCCAAGTCCATGCCAGGGTGTCGGGTAAGTGAAG
CCCGGTCCCCGTCACCATGGACCATTTCTTCTTTGTCTGTGAGCTCTCAGGCCACACTTATTCCTTCACCTTTAAAGTAG
AGAAGGAGGAAGATGCAGAGCATATGTCGGCATTAACTATGCTCTGCCTCACCAAGGGGGCAAAGGATAAGGATAATGTG
GTAGAAATTGTTGCCCAGCACCATGACCACCAGGAGATTGCAGTACCTGTGGCCAATCTCAAGTTGTCTTGCCAGCCCAT
GCTTAGTCTGGATGACTTTCAGCTTCAAATACCTGTGACTTTCCAGCTGACGTCCGGCTCTGGCCCTGTACAGATCACTG
GTTGGCACCAGATAGTTACTATAAGCAATGATGGTTCTGAAGATGATGAGAGTGAAGAGGAAGATGGAGAGGAGGAAGCT
GAGTTGTTCACTATCCTTCCTGCAAAAAGCAGAGGGGCAGG

Alignment

ORF - retro_dord_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.98 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGAAAALTFLSPESRVRAGGVRGQRSPAPVTMDSFFFGCELSGHTRSFTFKVEKEDDAEHVLALTMLC
          MA..AAA.L.FLS..S.V.A..V.G..SP.PVTMD.FFF.CELSGHT.SFTFKVEKE.DAEH..ALTMLC
Retrocopy MADSAAANLPFLSQGSQVHAR-VSGK*SPVPVTMDHFFFVCELSGHTYSFTFKVEKEEDAEHMSALTMLC

Parental  LTEGAKDECNVVEIVARNHDHQEIAVPVANLKLSCQPMLSLDDFQLQPPVTFRLKS-SGPVRITGRHQIV
          LT.GAKD..NVVEIVA..HDHQEIAVPVANLKLSCQPMLSLDDFQLQ.PVTF.L.S.SGPV.ITG.HQIV
Retrocopy LTKGAKDKDNVVEIVAQHHDHQEIAVPVANLKLSCQPMLSLDDFQLQIPVTFQLTSGSGPVQITGWHQIV

Parental  TISNDVSEDDESEEEDEEEEAELSPILPA-KKQKGR
          TISND.SEDDESEEED.EEEAEL..ILPA.KKQ.GR
Retrocopy TISNDGSEDDESEEEDGEEEAELFTILPA<KKQRGR

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_577 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577 ,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,