RetrogeneDB ID: retro_dord_460

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_201611:222..900(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000003759
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tuba4a
• Ensembl ID: ENSDORG00000000154
• Aliases: None
• Description: tubulin, alpha 4A [Source:MGI Symbol;Acc:MGI:1095410]

Sequence

>retro_dord_460
GAATGCATCTCCATCCACATGGGCCAGGCTGGTGGTCCAGATTGGGAATGCCTGTTGGGAGCTCTACTGCCTGGTACATA
GCATCCAGCCTGATAGCCAGATGTCAAGTGAGAAGACCATCGGGGGAGAGATGACTCCTTCAACACCTTCTTCAGTGAGA
CAGGTGCTGGCAAGCACGTGCTCAGGGCAGTGTTTGTAGACCTGGAGCCCACAGTCATTGATGAAGTTCAAACTGGCACC
TACGGTCAATTTTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCTGTGGTCACTACACCATTGGCAAGAA
GATCATTGACCTCATATTAAACCGGATCAGAAAACTGGCTGACCAGTGCACAGGTCTTCAGGGCTTCCTAGTCTTCCACA
GGTTTGATGGGGGAACTGGCTCTGGCTTTACCTCCCTACTGATGGAGCATCTCTCTGTGAACTATGGCAAGAAGTCCAAG
CTGGAGTTATCCATTTATCCTGCCCCCCACGTGTCCACAGCTGTAATTGAGCCCTACAACTCCATCCTCACCACCCTGGA
ACACTCTGATTTGTGCCTTCATGGTGGACAATGAGGCTATGACATCTGTTGTAGAAACCTTGATATTGAGCACCCAACCT
ACACTTACCTGAACCGCCTTATTAGCCAGATCGAGTCT

Alignment

ORF - retro_dord_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 52.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ECISVHVGQAG-VQMGNACWELYCLEHGIQPDGQMPSDKTIGGG-DDSFTTFFCETGAGKHVPRAVFVDL
          ECIS.H.GQAG.VQ.GNACWELYCL.H.IQPD.QM.S.KTIGG..DDSF.TFF.ETGAGKHV.RAVFVDL
Retrocopy ECISIHMGQAG>VQIGNACWELYCLVHSIQPDSQMSSEKTIGGE<DDSFNTFFSETGAGKHVLRAVFVDL

Parental  EPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFHS
          EPTVIDE...G.Y.Q.FHPEQLITGKEDA....A.GHYTIGK.IID..L.RIRKL.DQCTGLQGFLVFH.
Retrocopy EPTVIDEVQTGTYGQFFHPEQLITGKEDA----ACGHYTIGKKIIDLILNRIRKLADQCTGLQGFLVFHR

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSD-CAFMVDNEAI
          F.GGTGSGFTSLLME.LSV.YGKKSKLE.SIYPAP.VSTAV.EPYNSILTT...LEHSD.CAFMVDNEA.
Retrocopy FDGGTGSGFTSLLMEHLSVNYGKKSKLELSIYPAPHVSTAVIEPYNSILTT---LEHSD>CAFMVDNEAM

Parental  YDI-CRRNLDIERPTYTNLNRLISQIVS
          ....C.RNLDIE.PTYT.LNRLISQI.S
Retrocopy TSV<C-RNLDIEHPTYTYLNRLISQIES

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_460 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460 , retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,