RetrogeneDB ID: retro_dord_620

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_41656:446..1219(-)
• 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_620
AAGATCATCCATGGCAACAAGTCAATAGACTCTGGTATATCCTTGGATAGTAGTTACAAAATGAATTATCCTGAAATGGG
TGCATGTATAATAATTAATAATAAGAACTTTCATTACAGCATTGGAATGTCATCTCAGTTTGGTACATATGTAGACACGC
AACCCTCACAGAAACATTCCTTTACTTAAAATATGAAGTCAGGAATAAAAATGACATTCACATGAAGAAATTGTAGAATT
ATTGTACAATGTTTCTAAAGAAGATCATAACGAAAGATGCAGCTTTATTTGTGTAATTCTAAGACATGGTGAGGAAGGAA
TAATTTTTGGAACAAATGGACCTATTGACCTGAAAAAATTAACAAGTTTCTTCCGAGGAGATTATTGCAGAAGTCTAACT
GGGAAACCTAAGCTTTTCATCATTCAGGCCTGCTGGGGTACAGCACTAGACTATAGCATTGAGACAGATAGTGGTATTGA
TAATGACTTGACATGCCAGAAAATACCAGTAGAGGCTTACTTCCTGTATGCATAATCCCAGCGCCTGGTTACTATTCCTG
GTGAAATTCAAAGGATGGATCCTGGTTCATCCAGTCCCTTTGTGCTATGCTGAAACTCTATGAGAACAAGCTTGAACTGA
TACACATTCTTACATGGTTAACCACAAGGTAGCAACAGAATTCGAGTTCTTTTCCTTGGATTCCACGTTTCATGCAAAGA
AACAGATTCCATGTATTATGCCCATGCTCACAAAAGACCTGTATTTTTATCAC

Alignment

ORF - retro_dord_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 93.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KIIHGSKSMDSGISLDNSYKMDYPEMGVCIIINNKNFDKSTGMSPRSGTDVDA-ANLRETFLNLKYEVRN
          KIIHG.KS.DSGISLD.SYKM.YPEMG.CIIINNKNF..S.GMS...GT.VD..A.L.ETFL.LKYEVRN
Retrocopy KIIHGNKSIDSGISLDSSYKMNYPEMGACIIINNKNFHYSIGMSSQFGTYVDT<ATLTETFLYLKYEVRN

Parental  KNDL-TREEIVELLYNVSKEDHSKRSSFICVILSHGEEGIIFGTNGPVELKKLTSFFRGDYCRTLAGKPK
          KND....EEIVELLYNVSKEDH..R.SFICVIL.HGEEGIIFGTNGP..LKKLTSFFRGDYCR.L.GKPK
Retrocopy KNDI<SHEEIVELLYNVSKEDHNERCSFICVILRHGEEGIIFGTNGPIDLKKLTSFFRGDYCRSLTGKPK

Parental  LFIFQACRGTELDCGIETDSGTDDDMPCQKIPVEADFLYAYS-TAPGYYSWRNSKDGSWFIQSLCAMLKC
          LFI.QAC.GT.LD..IETDSG.D.D..CQKIPVEA.FLYA.S..APGYYSW.NSKDGSWFIQSLCAMLK.
Retrocopy LFIIQACWGTALDYSIETDSGIDNDLTCQKIPVEAYFLYA*S<PAPGYYSW*NSKDGSWFIQSLCAMLKL

Parental  YASKLELMHILT-RVNWKVAREYESFSLDSMFHAKKQIPCIVSMLTKDLYFHH
          Y..KLEL.HILT..VN.KVA.E.E.FSLDS.FHAKKQIPCI..MLTKDLYF.H
Retrocopy YENKLELIHILT<MVNHKVATEFEFFSLDSTFHAKKQIPCIMPMLTKDLYFYH

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_620 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,