RetrogeneDB ID: retro_dord_722

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_6293:54864..55352(+)
• Located in intron of: ENSDORG00000004377

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fhl1
• Ensembl ID: ENSDORG00000015644
• Aliases: None
• Description: four and a half LIM domains 1 [Source:MGI Symbol;Acc:MGI:1298387]

Sequence

>retro_dord_722
AAGTGCTTTGGCAAGTTCTGTGCCTGCGCCTGTGTGGAATGCCGCAAGCCCATCGGCCAGACTCCAAGGAAGTGCACTAC
AAGATCTGCTTCTGGCATGACTCGTGCTTCCGCTGTGCCAAGTGCTTTCGCCCCTTGGCCAGTGAGACCTTTGTGGCCAA
GGACAGCAATAATCTGTGCAACAACTGTGCCACTCGTGGGAAGACAACCCTCGGTGCAAAGGGTGCTTCAAGCCCTTGTG
GCAGGAGACCAGAACGTGGAGCACAAGGGCCTCATGTGGCACAAAGACTGCTTCACGTGCAGCAGCTGCAAGCAAGGCAT
GGGACGGGAAGCTTCTTCCCGAGAGGGGAGGACTTCTACTGTGTGACCTGCCATGAGACCAAGTTGGCCAAGCACTGCGT
GAAGTGCCACAAGGCCATCACATGTGGAGGAATCACTTACCAGGATCAGCCCTGGCATGCCGATTGCTGTGTGGGTGGTA
CCTGCTCG

Alignment

ORF - retro_dord_722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KCFDKFCANTCVECRKPIGA-DSKEVHYKNRFWHDSCFRCAKCFHPLANETFVAKDNKILCNKCATRG-E
          KCF.KFCA..CVECRKPIG..DSKEVHYK..FWHDSCFRCAKCF.PLA.ETFVAKD...LCN.CATRG.E
Retrocopy KCFGKFCACACVECRKPIGQ<DSKEVHYKICFWHDSCFRCAKCFRPLASETFVAKDSNNLCNNCATRG<E

Parental  DNPRCKGCFK-ALVAGDQNVEYKGLVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCHETKFAKHCVK
          DNPRCKGCFK.ALVAGDQNVE.KGL.WHKDCFTCS.CKQ..G.TGSFFP.GEDFYCVTCHETK.AKHCVK
Retrocopy DNPRCKGCFK<ALVAGDQNVEHKGLMWHKDCFTCSSCKQGMG<TGSFFPRGEDFYCVTCHETKLAKHCVK

Parental  CNKAITSGGITYQDQPWHADCFVCVTCS
          C.KAIT.GGITYQDQPWHADC.V..TCS
Retrocopy CHKAITCGGITYQDQPWHADCCVGGTCS

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_722 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722 ,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,