RetrogeneDB ID: retro_dord_691

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5633:2897..3476(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tfam
• Ensembl ID: ENSDORG00000014013
• Aliases: None
• Description: transcription factor A, mitochondrial [Source:MGI Symbol;Acc:MGI:107810]

Sequence

>retro_dord_691
CTTTCCAAGGGCCTGTGGGGCGCGCTGAGCGCACTGGGAAGATCTGGAGCGGAGCTGTGCACTGGCTGTGGGAGTCGCCT
GTATTCACCTTTAAGTTTTGTGTATTTTCCAAAATAGTTTTCATCCAACTTGAGTAGTTATCCAAAGAAACCCATGACTT
CCTACCTTCGATTGTATAAAGAACAGCTACCAGTATTTATAGCTCAGAACCCAGATGTAAAAAGTTAAGAACTAATTAGA
CAAATTGCAGAGGTATGGAGGGGACTTCCCTAATCAAAGAAAAAATATATGAAGATGCTTAAAAGACAGACTGGATAACA
TACAAAAAAAATAAACAATTCAAGGATAGCTTACTCCAAGTCAGCTTTTGTCTTTGGAAAAAGAAATCATACAAAGACGT
TTGAAAAGAAAAGTATTAATAAAAAGAGGGAGTTAACACCTCTTGGGAAAAAAAAACCTCATTCAGCTTACAACATTTTT
ATAGCTGAAAATTTTCCAGAAACCATAGATTCATCATCTAAGGAAAAACTGAACACATTAAATGAAAAAGCAGGTGTATT
ATCAACTTTCTGAAGACAA

Alignment

ORF - retro_dord_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.95 %
• Parental protein coverage: 79.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLRGVWGALRVLGRSGAELCTGCGSRLCSPFSFVY-PKWFSS-LSSYPKK-MTS-LRFSKEQLPVFRAQN
          L..G.WGAL..LGRSGAELCTGCGSRL.SP.SFVY.PK.FSS.LSSYPKK.MTS.LR..KEQLPVF.AQN
Retrocopy LSKGLWGALSALGRSGAELCTGCGSRLYSPLSFVYFPK*FSSNLSSYPKKPMTSYLRLYKEQLPVFIAQN

Parental  PDVKNKELIRQIAEVWRGLPESKKKIYEDAYKADWKIYKEEINRIQEQLTPSQLLSLEKEIIQRRLKRKI
          PDVK..ELIRQIAEVWRGLP.S.KK.Y....K..........N........S..............K..I
Retrocopy PDVKS*ELIRQIAEVWRGLP*S-KKKYMKMLKRQTG*HXXXXNNSRIAYSKSAFVFGKRNHTKTFEKKSI

Parental  IKKRELTSLGKPKKTRSAYNIFIAEKFPET-KSHLLEKLKILNEKWKNMPAFQKQ
          .KKRELT.LG......SAYNIFIAE.FPET..S...EKL..LNEK......F..Q
Retrocopy NKKRELTPLGXXXP-HSAYNIFIAENFPETIDSSSKEKLNTLNEKAGVLSTF*RQ

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_691 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691 ,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,