RetrogeneDB ID: retro_dord_409

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_1722:14410..14841(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arf1
• Ensembl ID: ENSDORG00000007603
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:MGI Symbol;Acc:MGI:99431]

Sequence

>retro_dord_409
CTGGGTGAGATCATGACCACCATCCCCACCATAGGTTTCAACGTGGAGACTGGTTGAGTACAAGAACATCAGCTTCCCTT
TGTGGGATATGGACAGCCAGGACAAGATCCAGCCACTGAGGCGTCACTACTTCCAGAACACCCAAGGCTTGATCTTTGTG
GTGGACAGCAATGACAGAGAGCATGTCAAGGAGGCGAGTGAATAGCTCATGCGGATGCTGGCGGAGGATGAGCTCCGGGA
TGTTGTCCTCCTGGTTTTTGCCAACAAGCAGGACCTCCCCAATGCCATGAATGATGTTGAAATCACAGACAAGCTGGGGC
TGCACTCTCTACACCACAGGAAACTGGTACATTCAGGCCACCTGTGCCATCAGCGGGGATGGGCTCTATGAAGGACTGGA
CTGGCTGTCCAATCAGCTCCGGAACCAGAAG

Alignment

ORF - retro_dord_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGEIVTTIPTIGFNVET-VEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREEL
          LGEI.TTIPTIGFNVET.VEYKNISF..WD...QDKI.PL.RHYFQNTQGLIFVVDSNDRE.V.EA.E.L
Retrocopy LGEIMTTIPTIGFNVET>VEYKNISFPLWDMDSQDKIQPLRRHYFQNTQGLIFVVDSNDREHVKEASE*L

Parental  MRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHR-NWYIQATCATSGDGLYEGLDWLSNQ
          MRMLAEDELRD.VLLVFANKQDLPNAMN..EITDKLGLHSL.HR.NWYIQATCA.SGDGLYEGLDWLSNQ
Retrocopy MRMLAEDELRDVVLLVFANKQDLPNAMNDVEITDKLGLHSLHHR>NWYIQATCAISGDGLYEGLDWLSNQ

Parental  LRNQK
          LRNQK
Retrocopy LRNQK

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_409 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dipodomys ordii	ENSDORG00000004312	1 retrocopy	retro_dord_731,
Dipodomys ordii	ENSDORG00000007603	4 retrocopies	retro_dord_31, retro_dord_351, retro_dord_409 , retro_dord_573,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,