RetrogeneDB ID: retro_dord_266

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6826:456467..457286(-)
• Located in intron of: ENSDORG00000014665

Retrocopy information

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

Parental gene information

• Parental gene symbol: Capza2
• Ensembl ID: ENSDORG00000016226
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 2 [Source:MGI Symbol;Acc:MGI:106222]

Sequence

>retro_dord_266
GTCCATATAGCAGCAAAGTTCATCATTCATGCCCCTCTTGGAGAATTTAATGAAGTTTTTAATGATGTTCGGTTATTGCT
TAATAATGATAATCTTCTCAGGGAAGGAGCAGCCCATGCATTTGCACAGTATAATTTGGACCAGTTTACACCAGTAAAAA
TTGAAGGTTATGAAGATCAGGTATTGATAACAGAACATGGTGACTTGGGAAATGGAAAGTTTTTGGATCCAAAAAACAGA
ATCTGCTTCAAATTTGATCACTTAAGAAAAGAAGCAACTGATCCAAGACCTTATGAAGCAGAAAATGCAATTGAATCATG
GAGAACTTCAGTAGAAACTGCTCTGCGAGCTTATGTAAAAGAACATTACCCAAATGGGTTCTGCACTGTGTATGGTAAAA
AAATAGATGGACAACAAACCATTATCGCATGTATGGAAAGCCATCAGTTCCAAGCAAAAAATTTTTGGAATGGTCGTTGG
ATGTCAGAATGGAAGTTTACAGTCAGTCCTTCAAGCACTCAAGTGGTTGGCATCTTGAAAATTCAGGTTCATTATTATGA
ACATGGTAATGTTCAACTAGTGAGTCATAAAGATATACAAGATTTTCTAACAGTGTCTAATGAGGTGCAAAGAGCAAAAG
AATTTATAAAGATTGTAGAAGCTGTAGAAAATGAATACCAGACTGCCATCAGTGAGAATTACCAGACAATGTCAGACACT
ACTTTCAAAGCCTTACATCGACAGTTGCCAGTTACACGTACTAAGATTGATTGGAACAAGATCCTTAGCTACAAGATCGG
CAAAGAGATGCAGAATGCG

Alignment

ORF - retro_dord_266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRIAAKFIIHASPGEFNEVFNXXXXXXXXXXXXXXXXXXAFAQYNLDQFTPVKIEGYEDQVLITEHGDLG
          V.IAAKFIIHA..GEFNEVFN..................AFAQYNLDQFTPVKIEGYEDQVLITEHGDLG
Retrocopy VHIAAKFIIHAPLGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNLDQFTPVKIEGYEDQVLITEHGDLG

Parental  NGKFLDPKNRICFKFDHLRKEATDPRPYEAENAIESWRTSVETALRAYVKEHYPNGVCTVYGKKIDGQQT
          NGKFLDPKNRICFKFDHLRKEATDPRPYEAENAIESWRTSVETALRAYVKEHYPNG.CTVYGKKIDGQQT
Retrocopy NGKFLDPKNRICFKFDHLRKEATDPRPYEAENAIESWRTSVETALRAYVKEHYPNGFCTVYGKKIDGQQT

Parental  IIACIESHQFQAKNFWNGRWRSEWKFTVSPSSTQVVGILKIQVHYYEDGNVQLVSHKDIQDFLTVSNEVQ
          IIAC.ESHQFQAKNFWNGRW.SEWKFTVSPSSTQVVGILKIQVHYYE.GNVQLVSHKDIQDFLTVSNEVQ
Retrocopy IIACMESHQFQAKNFWNGRWMSEWKFTVSPSSTQVVGILKIQVHYYEHGNVQLVSHKDIQDFLTVSNEVQ

Parental  TAKEFIKIVEAAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
          .AKEFIKIVEA.ENEYQTAISENYQTMSDTTFKAL.RQLPVTRTKIDWNKILSYKIGKEMQNA
Retrocopy RAKEFIKIVEAVENEYQTAISENYQTMSDTTFKALHRQLPVTRTKIDWNKILSYKIGKEMQNA

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_266 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 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266 ,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,