RetrogeneDB ID: retro_dord_178

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4606:32591..33249(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Casp3
• Ensembl ID: ENSDORG00000002554
• Aliases: None
• Description: caspase 3 [Source:MGI Symbol;Acc:MGI:107739]

Sequence

>retro_dord_178
ATGGAGAACACTGAAAATTCAGTGGACTTAAAGTCCATTAAAACTTTTGAAACAAAGATCATCTATGGCAGCAAATCAAT
GGACTCTGGGATATCCTTGGATAGTAGTTACAAAATTGATTATCCTGAAATAATTAATAATAACTTTCATAAAAGCACTG
GAATGGCACCTCAGTATGGCACAGATACAGACACCACAGCAGCCCTCAGAGAAACATTCCTGAACTGGAAATACAAAGTC
AGTAATAAAAATGACCTTACACATGAAGAAATTGTAGAATTATTAAACAAAGTTTCTAAAGAATATCATAGCAAAAGGAG
CAGCAGCTTTACTTGTGTAATTCTGAGTCATGATGAGGAAGGAAAAATTTTCTGGAACAAATAGACCTGTTGACCTAAAA
TTAACAAGCTTCTGCCAAGGAGATTATTGCAGAAGTCTAACTGGAAAACCTAAGCCTTTCATCATTCAGTTCTGGTAGGA
TACAGAACTAGACTGTGGCATTGAGACTGATAGTGATATTGATGATGACATAGCCTGCCAGAAAATATCAGTAGAGGCTG
ACTTCCTGTGTGTAGATTCTACAGCACCTGGTTATTATTCCTGGCAAAAGCCCAAGGATGGATCCTGGTTCATCCAGACC
CTTTGTGCTAAGCTGAAA

Alignment

ORF - retro_dord_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.45 %
• Parental protein coverage: 80.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENSENSVDSKSIKTFETKIIHGSKSMDSGISLDNSYKMDYPEMGVCIIINNKNFDKSTGMSPRSGTDVD
          MEN.ENSVD.KSIKTFETKII.GSKSMDSGISLD.SYK.DYPE....II.NN..F.KSTGM.P..GTD.D
Retrocopy MENTENSVDLKSIKTFETKIIYGSKSMDSGISLDSSYKIDYPE----IINNN--FHKSTGMAPQYGTDTD

Parental  -AANLRETFLNLKYEVRNKNDLTREEIVELLYNVSKEDHSKR-SSFICVILSHGEEGIIF-GTNGPVELK
          ..A.LRETFLN.KY.V.NKNDLT.EEIVELL..VSKE.HSKR.SSF.CVILSH.EEG.IF.GTN.PV.L.
Retrocopy TTAALRETFLNWKYKVSNKNDLTHEEIVELLNKVSKEYHSKRSSSFTCVILSHDEEGKIF>GTNRPVDL-

Parental  KLTSFFRGDYCRTLAGKPKLFIFQACRGTELDCGIETDSGTDDDMPCQKIPVEADFLYAYSTAPGYYSWR
          KLTSF..GDYCR.L.GKPK.FI.Q....TELDCGIETDS..DDD..CQKI.VEADFL...STAPGYYSW.
Retrocopy KLTSFCQGDYCRSLTGKPKPFIIQFW*DTELDCGIETDSDIDDDIACQKISVEADFLCVDSTAPGYYSWQ

Parental  NSKDGSWFIQSLCAMLK
          ..KDGSWFIQ.LCA.LK
Retrocopy KPKDGSWFIQTLCAKLK

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_178 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178 , retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,