RetrogeneDB ID: retro_dord_769

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_8622:51451..51976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hax1
• Ensembl ID: ENSDORG00000012587
• Aliases: None
• Description: HCLS1 associated X-1 [Source:MGI Symbol;Acc:MGI:1346319]

Sequence

>retro_dord_769
GAACTTCCAGGTCCTGAGTCAGAGACACCTGGTGAGAGACTGCGGGAGGGGCAGATGCTTCCGGACTCAATGCTTAAATA
CCCAGATAGTCATCAGCCCAAGATCTTTGGGGGGGGGGTCTTGGAGAGTGATACAAGAACTGAAACCTCCAAACCAGCAC
CAGACTGGGGGTCCCCGAGACCTTTTCATAGGTTTGATGATATGTGGCCTGTGACTCCCCATCCTAGAGCCAGAGAGGAC
AATGATCTTGATTCCCAGGTTTCCCAGGAAGGTCTTGGTCCTGTTCTGCAGCCTCAGCCCAAGTCCTACTTCAAGAGTAT
CTCTGTGACCAAGATCACAAAACCAGATGGGAAAGTGGAAGAGCACCGGACTATAGTGGACAGTGAGGGTCGGAGGGAGA
CCACAATAACTCACCAAGAAGCAGATGGCAGCCTTAGAGTTGATCCAGAATCACCAAGACCTCCAGCCTTAGATGATGCC
TTTTCCATCCTTGATTTATTTCTAGGACGTTGGTTCGGGCCCCGT

Alignment

ORF - retro_dord_769 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.57 %
• Parental protein coverage: 63.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELPGPESETPGERLREGQTLRDSMLKYPDSHQPKIFGGA-LESDTRTETSKPAPDWGSPRPFHRFDDMWP
          ELPGPESETPGERLREGQ.L.DSMLKYPDSHQPKIF....LESDTRTETSKPAPDWGSPRPFHRFDDMWP
Retrocopy ELPGPESETPGERLREGQMLPDSMLKYPDSHQPKIFXXXXLESDTRTETSKPAPDWGSPRPFHRFDDMWP

Parental  VTPHPRAREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGKVEEHRTIVDSEGRRETTITHQE
          VTPHPRAREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGKVEEHRTIVDSEGRRETTITHQE
Retrocopy VTPHPRAREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGKVEEHRTIVDSEGRRETTITHQE

Parental  ADGSLRVDPESPRPPALDDAFSILDLFLGRWFGPR
          ADGSLRVDPESPRPPALDDAFSILDLFLGRWFGPR
Retrocopy ADGSLRVDPESPRPPALDDAFSILDLFLGRWFGPR

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_769 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769 ,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,