RetrogeneDB ID: retro_dord_11

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_26122:3772..4903(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000006870
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Actb
• Ensembl ID: ENSDORG00000010079
• Aliases: None
• Description: actin, beta [Source:MGI Symbol;Acc:MGI:87904]

Sequence

>retro_dord_11
ATGGTTGATGATGAGCTGACCGCCTTGGTAGTAGACAATGGGTCAGGGATGTGCAAGGCAGGTTTTGGAGGTGACGATGC
CCCCAGAGCAGTGTTCCCCTCCATGGTAGGGCGTCCTCGGCACCAGGGCGTCATGGTGGGCATGGGCCAGAAGGACTGCT
ATGTGGGAGATGAGGCCCAGAGTAAGAGAGGCATTCTGACCCTGAAGTATCCCATCGAACACGGCGTTGTCACCAACTGG
GATGATATGGAGAAGATCTGGTATCACACCTTCTACAACGAGCTCCGCGTGGCACCCGATGAGCACCCCATCCTCCTCAC
CGAGGCGCCCCTCAACCCCAAGATCAACCGGGAAAAGATGACTCAGATCATGTTCGAGGCCTTCAACACACCTGCCATGT
ACGTGGCTATCCAAGCCGTGCTGTCCCTCTATGCCTCGGGACGGACCACAGGTATTGTGATGGATTCTGGAGATGGGGTT
ACTCACACGGTGCCCATCTACGAGGGCTACGCCCTGCCCCATGCTATTCTACGTCTAGATCTGGCAGGTAGAGACCTGAC
AGATTACCTCATGAAGATCCTGACAGAACGAGGTTACAACTTCACCACCACAGCCGAGCGAGAGATTGTGCGAGATGTCA
AAGAGAAATTGTGTTATGTAGCCCTGGACTTTGAGCAAGAGATGCTCAGTGCCGCTACATCCTCTTCACTTGAAAAAAGC
TACGAGCTTCCTGATGGGCAGGTAATCACCATAGGGAATGAACGCTTTCGATGCCCTGAAGCCGTTTTCCAGCCATCCTT
TCTGGGCCTTGAGTCCAGCGGAATCCACGAGGCAACCTTCAACTCCATCATGAAGTGCGATGTGGATATCCGCAAGGATC
TCTATGCCAACACCGTGCTGTCTGGGGGCAGCACCATGTACCCAGGAATTGCTGACCGGATGCAGAAGGAAATTATAGCC
CTGGCACCTAGCACCATGAAAATCAAGATCATAGCCCCCCCAGAGCGCAAGTATTCTGTTTGGATTGGAGGCTCCATCCT
GGCCAGCCTGTCCACATTCCAGCAGATGTGGATTAGTAAGCAGGAATATGATGAGGCTGGTCCTCCCATCGTTCACAGAA
AATGCTTCTGA

Alignment

ORF - retro_dord_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          .DD...ALVVDNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYP
Retrocopy VDDELTALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
          IEHG.VTNWDDMEKIW.HTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVL
Retrocopy IEHGVVTNWDDMEKIWYHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVL

Parental  SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGY.FTTTAEREIVR
Retrocopy SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYNFTTTAEREIVR

Parental  DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
          D.KEKLCYVALDFEQEM..AA.SSSLEKSYELPDGQVITIGNERFRCPEA.FQPSFLG.ES.GIHE.TFN
Retrocopy DVKEKLCYVALDFEQEMLSAATSSSLEKSYELPDGQVITIGNERFRCPEAVFQPSFLGLESSGIHEATFN

Parental  SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIMKCDVDIRKDLYANTVLSGG.TMYPGIADRMQKEI.ALAPSTMKIKIIAPPERKYSVWIGGSILASLS
Retrocopy SIMKCDVDIRKDLYANTVLSGGSTMYPGIADRMQKEIIALAPSTMKIKIIAPPERKYSVWIGGSILASLS

Parental  TFQQMWISKQEYDESGPSIVHRKCF
          TFQQMWISKQEYDE.GP.IVHRKCF
Retrocopy TFQQMWISKQEYDEAGPPIVHRKCF

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_11 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 13 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11 ,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,