RetrogeneDB ID: retro_dord_414

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1729:82842..83978(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Trnt1
• Ensembl ID: ENSDORG00000014035
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:MGI Symbol;Acc:MGI:1917297]

Sequence

>retro_dord_414
TTATTTGTGAAAGAGAATCAAGAGCTGAGAACAGCAGAAGGAGCTGTGAGGGATCTGCCGAATGGGGTGAAACTTCGAGA
TGTCGATTTTGCCACCCCAACCCAAATGAAGGAGATGTTTCCGTCAGGCAGCATTCGGATGACCAACAAGGGAGAGAAGC
ATGGAACCATCACAGCCAGGCTTCGTGAAGACAATTTTGAAATTACCACACTAAGGATGGATGTCACAACTGACGGAAGA
CATGCCTAGGTAGAATTCACAACTGCCGGACAGAAGGATGCTGAACACAGAGACCTCACTATAAACTCCATGTTTCTAGG
CCTTGATGGTTCTTGATTTAATTACTTTAATGGCTATGAAGATTTTAAAAAAATAAGAAAGTTACGATTTGTAGGACACA
CACATCAAAGAATACACAAAGATTAACTTCGGATTTTAAGCTACTTCAGGTTTAATGGCAGAATTGTGGACAAACCTGGT
GAACATGATGCTGAGCAATCGCAGAAAATGCGAAAGGCTTGGCTGGACTATCAGGAGAGTGCATTTGGGTAGAACTGAAA
AAAATTCTTGTTGGTAAATGTGTAAACGACTTATTTCACCTGATCTATGATCTTGATGTGGCTCCTCATATAGGTTTACC
CACAATTGCAAGTTTAGAAGAATTTAGTGAAGTCAGTAAAAATGTTGAAAGTTGCTCAGCAAAGCCAAGGACCATCTTGG
CCTCACTGCAGAAAGTACAAGATGATGTCACAAAATGTGATTTGCGGTTGAAGATTTCAAAAGAAGAGGAAAAACCTTGG
CTTATTTAGAGTTAAAAATAAGAAAGACTTAGTTAAAGCATCAGATTGTTCTGAACCATTGAAACCCTATCAAAACTTCA
TGGTAGATTCCAGAGAGCCAGATGCAAGTGCCCGAGTATGTGAGCTGCTGAAGTACCAGAGTGAACGCAGTCTCCTCATG
GAGATGCAGCAGCGGTCCCTGCCCCCTTCCCTATGAGCAGACATGACATTAGAAAAGTGGGCATTTCTTCCCGGAAGGAA
ACTGGTGCTGTGTTACAGCAACTGCATGAACAGTGAAAAAAAAAAAGTGGCTGCCAAATGGAAAAAGAGGAATTCCTAAG
TTACATAAAGAAGACC

Alignment

ORF - retro_dord_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFVKENHELRIAGGAVRDLLNGVKPQDVDFATTATPTQMKEMFQSAGIRMINNKGEKHGTITARLHEENF
          LFVKEN.ELR.A.GAVRDL.NGVK..DVDF...ATPTQMKEMF.S..IRM..NKGEKHGTITARL.E.NF
Retrocopy LFVKENQELRTAEGAVRDLPNGVKLRDVDF---ATPTQMKEMFPSGSIRM-TNKGEKHGTITARLREDNF

Parental  EITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKN-KKVRFVGHAHQ
          EITTLR.DVTTDGRHA.VEFTT..QKDAE.RDLTINSMFLG.DG..F.YFNGYED.K...K.RFVGH.HQ
Retrocopy EITTLRMDVTTDGRHA*VEFTTAGQKDAEHRDLTINSMFLGLDGS*FNYFNGYEDFKKIRKLRFVGHTHQ

Parental  RIQEDYLRILRYFRFYGRIVDKPGEHDPETLEAI-AENAKGLAGISGERIWVELKKILVGNHVNHLIHLI
          RI..D.LRIL.YFRF.GRIVDKPGEHD.E......A....GL...SGE.IWVELKKILVG..VN.L.HLI
Retrocopy RIHKD*LRILSYFRFNGRIVDKPGEHDAEQSQKM<AKGLAGL---SGECIWVELKKILVGKCVNDLFHLI

Parental  YDLDVAPHIGLPTPSSLEEFNQVSKNVEGCSAKPMTILASLLKVQDDVTKLDLRLKISKEE-KNLGLFIV
          YDLDVAPHIGLPT..SLEEF..VSKNVE.CSAKP.TILASL.KVQDDVTK.DLRLKISKEE.KNLGLF.V
Retrocopy YDLDVAPHIGLPTIASLEEFSEVSKNVESCSAKPRTILASLQKVQDDVTKCDLRLKISKEE>KNLGLFRV

Parental  KNRKDLVKASDSSEPLKPYQDFIIDSREPDASARVCELLKYQGERGLLKEMEQWSIP-PFPVSGHDIRKV
          KN.KDLVKASD.SEPLKPYQ.F..DSREPDASARVCELLKYQ.ER.LL.EM.Q.S.P.PFP.S.HDIRKV
Retrocopy KNKKDLVKASDCSEPLKPYQNFMVDSREPDASARVCELLKYQSERSLLMEMQQRSLP<PFPMSRHDIRKV

Parental  GISSGKEIGALLQQLREQ-WKKSGYQMEKEELLSYIKKT
          GISS.KE.GA.LQQL.EQ.....G.QMEKEE.LSYIKKT
Retrocopy GISSRKETGAVLQQLHEQXXXXXGCQMEKEEFLSYIKKT

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_414 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014035	1 retrocopy	retro_dord_414 ,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Rattus norvegicus	ENSRNOG00000006432	1 retrocopy	retro_rnor_512,