RetrogeneDB ID: retro_dord_312

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_111269:1323..1691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc3
• Ensembl ID: ENSDORG00000008212
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3 [Source:MGI Symbol;Acc:MGI:1928375]

Sequence

>retro_dord_312
GCCTACCATTCTCTCATGGACCCAGACCCAAGCTCATTGGCAACATGGCGCTGCTGCCTATCCGAAGTCAGTTCAAAGGA
CCTGCCCCTCATGAGACAAAAGACACTGACATCGTGGATGAAGCCATCTATTACTTTAAGGCTAACGTGTTCTTCAAAAA
CTATGAAATTAAAAATGAAGCTGATAGAACCTTGATACCTATAACTCTCTACATTTCTGAGCATCTAAAGAAACTCCAAA
AGTGCATCTCCAGAAGCCAGGGCGAGAAGGAGATGTACATGCTGGGAATCACCCACTTCCCTATCCCCGGCCAGCCTGGG
TTTCCCCTCAATGCCATTTATGCCAAGCCTGCGACCAAACAGGAGGAC

Alignment

ORF - retro_dord_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AYHSSLMDPDT-KLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYI
          AYHS.LMDPD..KLIGNMALLPIRSQFKGPAP.ETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLI.I
Retrocopy AYHS-LMDPDP<KLIGNMALLPIRSQFKGPAPHETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIPI

Parental  TLYISECLKKLQKCNSRSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPATKQED
          TLYISE.LKKLQKC.SRSQGEKEMY.LGIT.FPIPG.PGFPLNAIYAKPATKQED
Retrocopy TLYISEHLKKLQKCISRSQGEKEMYMLGITHFPIPGQPGFPLNAIYAKPATKQED

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_312 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Dasypus novemcinctus	ENSDNOG00000004987	2 retrocopies	retro_dnov_2619, retro_dnov_685,
Dipodomys ordii	ENSDORG00000008212	1 retrocopy	retro_dord_312 ,
Erinaceus europaeus	ENSEEUG00000011531	2 retrocopies	retro_eeur_122, retro_eeur_99,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Procavia capensis	ENSPCAG00000011858	2 retrocopies	retro_pcap_421, retro_pcap_441,
Pongo abelii	ENSPPYG00000004947	6 retrocopies	retro_pabe_1735, retro_pabe_1790, retro_pabe_2838, retro_pabe_376, retro_pabe_769, retro_pabe_792,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Tupaia belangeri	ENSTBEG00000011219	1 retrocopy	retro_tbel_2268,
Tarsius syrichta	ENSTSYG00000002953	4 retrocopies	retro_tsyr_1150, retro_tsyr_1341, retro_tsyr_2103, retro_tsyr_794,