RetrogeneDB ID: retro_shar_144

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834465.1:1394021..1394528(+)
• Located in intron of: ENSSHAG00000012191

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSSHAG00000014805
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_shar_144
TATTCCTCTCTTATGGACCCTGATACCAAACTAATTGGAAACATGGCACTGTTACCTATTGGAAGTCAATTTAAGGAGAG
CTCCAAAAGAAACAAAAAGACACAGATACTGTGGTTAAAGCTATCTATTATTTCCAGAGCCTGTCTTCTTCAAAAACTAT
GAAATTAAGAATGAAACTGATAGGACATTGATCTATATAACTCTTTACATTTCTGAATACTTAAAGAAACTCCAGAATTA
CAACTCAAAAAGATAAGGAGAGAAATTAATTTATACATTGTGAATCACTAGTTTTCCTATTCCTGGAAAGCCAGATTTCT
CTCTTATTGCCATTTATGCCAAACCTTAAAATAAGCTAGAACATGAAATGATTAGGGTCTATTTACAACAACTGTGGCAA
GAAAATGGCCCAAGGCTTGTGAAAAGGTCTTTGATCCTCAAAGTGACAGATTTAGCAAGTGGTGGACTTGCTTTGTAAAG
AAGCAGTTCATGAACAAGAATCTGAGT

Alignment

ORF - retro_shar_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.57 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HSSLMDPDTKLIGNMALLPIRSQFK-GPAPRETKDTDIVDEAIYYFKA-NVFFKNYEIKNEADRTLIYIT
          .SSLMDPDTKLIGNMALLPI.SQFK.G......KDTD.V..AIYYF....VFFKNYEIKNE.DRTLIYIT
Retrocopy YSSLMDPDTKLIGNMALLPIGSQFK<GELQKKQKDTDTVVKAIYYFQS<PVFFKNYEIKNETDRTLIYIT

Parental  LYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQETGL
          LYISE.LKKLQ..NSK..GEK..YTL.IT.FPIPG.P.F.L.AIYAKP.NK.E.E..R.YLQQL.QE.G.
Retrocopy LYISEYLKKLQNYNSKR*GEKLIYTL*ITSFPIPGKPDFSLIAIYAKP*NKLEHEMIRVYLQQLWQENGP

Parental  RL-CEKVFDPQSDKPSKWWTCFVKRQFMNKSLS
          RL.CEKVFDPQSD..SKWWTCFVK.QFMNK.LS
Retrocopy RL<CEKVFDPQSDRFSKWWTCFVKKQFMNKNLS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_144 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 27 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
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,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431, retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Loxodonta africana	ENSLAFG00000006166	3 retrocopies	retro_lafr_1119, retro_lafr_763, retro_lafr_840,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009, retro_mmur_1507,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Nomascus leucogenys	ENSNLEG00000002802	4 retrocopies	retro_nleu_239, retro_nleu_283, retro_nleu_3078, retro_nleu_389,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Otolemur garnettii	ENSOGAG00000013424	1 retrocopy	retro_ogar_2855,
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,
Sorex araneus	ENSSARG00000000546	2 retrocopies	retro_sara_529, retro_sara_601,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144 , retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177,
Ictidomys tridecemlineatus	ENSSTOG00000011979	1 retrocopy	retro_itri_1350,
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,
Tursiops truncatus	ENSTTRG00000015083	2 retrocopies	retro_ttru_713, retro_ttru_880,
Vicugna pacos	ENSVPAG00000008404	1 retrocopy	retro_vpac_225,