RetrogeneDB ID: retro_dord_331

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_119335:311..803(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Isy1
• Ensembl ID: ENSDORG00000006886
• Aliases: None
• Description: ISY1 splicing factor homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1923310]

Sequence

>retro_dord_331
GAACGAAGACCTTTCCTTGCTTCAGAACGTACAGAGTTGCCCAAAGCAGAGAAGTGGAGACAACAGATTATTGGAGAGAT
CTCCAAAAAAGTAGCTCAGATTCAGAATGCTGGTTTGGGTGAATTCCAAATTTGAAACCGGAATGATGAGATCAGTAAGT
TGTTAAGAGAAAAAGGTCACTGGGAGGTGCGGATAAAAGAACCTGACGGCCCTGATTATGGGAAAGTTGGTCCTAAAATG
CTGGATCATGAAGGGAAAGCAGTCCCAGGAAACCGAGGTTACAAGTACTTTGGAGCAGCAAAGGATTTACCTGGTGTTAG
AGAGCTGTTTGAAAAAGAACCTCTTCCTCCTCCCAGAAAGACACGTGCTGAGCTGATGAAGGCAATTGATTTTGAATACT
ATGGTTACCTAGATGAAGATGATGGTGTTACTGTACCTTTGGAGCAAGAATATGAAAAGAAACTGAGAGCTGAGCTGGTG
GAAAAATGGAAA

Alignment

ORF - retro_dord_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERRPFLASECTELPKAEKWRRQIIGEISKKVAQIQNAGLGEFRIRDLNDEINKLLREKGHWEVRIKELGG
          ERRPFLASE.TELPKAEKWR.QIIGEISKKVAQIQNAGLGEF.I...NDEI.KLLREKGHWEVRIKE..G
Retrocopy ERRPFLASERTELPKAEKWRQQIIGEISKKVAQIQNAGLGEFQI*NRNDEISKLLREKGHWEVRIKEPDG

Parental  PDYGKVGPKMLDHEGKEVPGNRGYKYFGAAKDLPGVRELFEKEPLPPPRKTRAELMKAIDFEYYGYLDED
          PDYGKVGPKMLDHEGK.VPGNRGYKYFGAAKDLPGVRELFEKEPLPPPRKTRAELMKAIDFEYYGYLDED
Retrocopy PDYGKVGPKMLDHEGKAVPGNRGYKYFGAAKDLPGVRELFEKEPLPPPRKTRAELMKAIDFEYYGYLDED

Parental  DGVIVPLEQEYEKKLRAELVEKWK
          DGV.VPLEQEYEKKLRAELVEKWK
Retrocopy DGVTVPLEQEYEKKLRAELVEKWK

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_331 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006886	1 retrocopy	retro_dord_331 ,
Ficedula albicollis	ENSFALG00000000023	1 retrocopy	retro_falb_5,
Loxodonta africana	ENSLAFG00000004015	2 retrocopies	retro_lafr_1070, retro_lafr_1170,
Myotis lucifugus	ENSMLUG00000011804	1 retrocopy	retro_mluc_1401,
Oryctolagus cuniculus	ENSOCUG00000003923	1 retrocopy	retro_ocun_1485,
Taeniopygia guttata	ENSTGUG00000003998	1 retrocopy	retro_tgut_5,