RetrogeneDB ID: retro_dord_390

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_156696:2..369(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zmynd19
• Ensembl ID: ENSDORG00000008360
• Aliases: None
• Description: zinc finger, MYND domain containing 19 [Source:MGI Symbol;Acc:MGI:1914437]

Sequence

>retro_dord_390
CCATGGGGCTGGCGACCTTAAAGCAGAAGAGACCTCCAGCAAACAGAGAGAGCAAAGCTTGTACTGGCTTGCAATCCAGC
AGCTGCCCACGGACCCCATAGAAGAGCAGTTCCCTGTCCTGAACGTGACGCGGTACTACAGTGCCAATGGGGATGTGGTA
GAGGAGGAGGAAAACTCCTGCACCTACTATGAATGTCATTACCCTCCTTGCACAGTAACTGAGAAGCAGCTTCTGGAGTT
CAACATCTGTGGGCGTTGCCAGGTGGCATGGTACTGTGGTTCCCAGTGCCAGCAGAAGGACTGGCCTGCCCACAAGAAGC
ACTGTGGAGAGAGGAAGCGTCCCTTCCAGCATGAGTTCGAGCAGGAG

Alignment

ORF - retro_dord_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 58.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PWGWRP-KAEETSSKQREQSLYWLAIQQLPTDPIEEQFPVLNVTRYYNANGDVVEEEENSCTYYECHYPP
          PWGWRP.KAEETSSKQREQSLYWLAIQQLPTDPIEEQFPVLNVTRYY.ANGDVVEEEENSCTYYECHYPP
Retrocopy PWGWRP>KAEETSSKQREQSLYWLAIQQLPTDPIEEQFPVLNVTRYYSANGDVVEEEENSCTYYECHYPP

Parental  CTVIEKQLREFNICGRCQVARYCGSQCQQKDWPAHKKHCRERKRPFQHELEPE
          CTV.EKQL.EFNICGRCQVA.YCGSQCQQKDWPAHKKHC.ERKRPFQHE.E.E
Retrocopy CTVTEKQLLEFNICGRCQVAWYCGSQCQQKDWPAHKKHCGERKRPFQHEFEQE

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_390 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
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390 ,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,