RetrogeneDB ID: retro_dord_182

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4783:141325..142045(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000006582
• Aliases: None
• Description: None

Sequence

>retro_dord_182
ATGAGCTTCTGGGTGGAGATTGTGGACCAAGCTTCCCTAGATCTCTTCAAGGGAGTCATTCACATGTTAGCCGACCTCAC
TAATGGCTGCATTCTCTGCAGCTGCCTGGATAAACTGAGCTTCATTCTTTTGGGGAAGCCAGAAAGTGGAGGAGTGAACA
TGTGGTGTGAGTTCAGGCAGAACTTTTTCAGCACATTTGAAATGGCAGATGTCTCTGTAGAAAGTGACATGTATTTACAA
CTATGTTTGGAAAACATATCTGGAGCCTGGAAAAGTGCCCACAATGGCAAAGCCATAAAATCATGCTGTCTAATGAACAC
TCTGGGAGCCTCAAGATCTGTGTGAAGCTGCTATTTGTGTCTGGCAGGAGTTGTACAGTGACAAAATACTTCCCCATAGA
CGTTATGCCTACCAATTTGTGGAACGAAATACAAGAACCGACAGTTGCAGACTTGGATATTAGCATTTATTTGCCAGTCT
TGAAGACTATGAAGACATAATGACATGATGTGAAAACAATGGAAACCGATTGGCAATCACCTTGTTATGGAAGCAAACCA
AAATGGAGAATTGAACCTGAAGATAGAAAGTATATCAGTAAGTATTACCACTTATTTTAAGAAGCTTAGACATCCTCCAT
TAGCTTTTGAGAATGACTCTGAAGACAGAGAACTGGAAGAGAGGACTGTGGTGCACATAGCTGTCAAGCAGGTACTCCAA

Alignment

ORF - retro_dord_182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 85.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRFNAEIVDKHSLDDFKRVINMLTNLAKGCILHICPDKLNFILLGSPESGGASLWCELPQENFFSTFQMQ
          M.F..EIVD..SLD.FK.VI.ML..L..GCIL..C.DKL.FILLG.PESGG...WCE..Q.NFFSTF.M.
Retrocopy MSFWVEIVDQASLDLFKGVIHMLADLTNGCILCSCLDKLSFILLGKPESGGVNMWCEFRQ-NFFSTFEMA

Parental  GISAEYNEIYLQVQLENITRVVNTPHSTETLR-IKFINKYSGILKFCIKQLPESNRSRTMTYYFPIVVIP
          ..S.E....YLQ..LENI.......H.......I...N..SG.LK.C.K.L..S.RS.T.T.YFPI.V.P
Retrocopy DVSVE-SDMYLQLCLENISGAWKSAHNGKAIK<IMLSNEHSGSLKICVKLLFVSGRSCTVTKYFPIDVMP

Parental  TNFWNELQEPIVPDLDVSIY---LPVLKTMKNIVEKM-KNISNHLVIEANLNGELNLKIETELVCVTTHF
          TN.WNE.QEP.V.DLD.SIY...L...KT....V..M.K.I.NHLV.EAN.NGELNLKIE...V..TT.F
Retrocopy TNLWNEIQEPTVADLDISIYLPVLKTMKT**HDVKTM>KPIGNHLVMEANQNGELNLKIESISVSITTYF

Parental  KGLGNPPLASQS-CRDRSPGELTEVHIEIKKLLQ
          K.L..PPLA......DR...E.T.VHI..K..LQ
Retrocopy KKLRHPPLAFENDSEDRELEERTVVHIAVKQVLQ

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_182 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001764	4 retrocopies	retro_chof_1438, retro_chof_1958, retro_chof_2084, retro_chof_898,
Dipodomys ordii	ENSDORG00000006582	1 retrocopy	retro_dord_182 ,
Echinops telfairi	ENSETEG00000009941	2 retrocopies	retro_etel_1764, retro_etel_1797,
Nomascus leucogenys	ENSNLEG00000004497	1 retrocopy	retro_nleu_2321,
Oryctolagus cuniculus	ENSOCUG00000027263	1 retrocopy	retro_ocun_761,
Otolemur garnettii	ENSOGAG00000012683	1 retrocopy	retro_ogar_1,
Pongo abelii	ENSPPYG00000025821	1 retrocopy	retro_pabe_151,
Sorex araneus	ENSSARG00000012348	1 retrocopy	retro_sara_391,
Ictidomys tridecemlineatus	ENSSTOG00000027204	1 retrocopy	retro_itri_151,