RetrogeneDB ID: retro_etel_1323

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_247179:12873..13402(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSETEG00000006992
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_etel_1323
ATACCAGCCTATCATTCCTCTATCATTGACTGGGACACAAACCTCATTGGAAACATGGCCCTGCTACCTATCAGAAGTCA
GTTCAAAGGATGAGTCCCTCAAGAGACAAAAGATACATATATTGTCCATGAGGCTATCTTTTAGTTCAAGGTGAACGTTT
TCTTCCAAAACATTGAAATGAAAAATGAAGCAGACAGGACCTTCATATGTATCACTCCCTACAGTTCTGAATGCCTAAGG
AAACTGCAGAAGTGCAATTCCAAAGCCAAGGTGAGAAAGAAGTTACACACTGGGTATCACTACCTTCCTCATTCCTAGAA
AGCCCAGGTTTCCACTGAATGTCATTTATGCCAAACCTGAAAGCAAGCAGGAAGATGATATGAAGGCCTATTTGTAGCAT
TTAAGTCAAGAAACAGGACTGAGACTTCGTGAGAAAATATTTGACCCTCAGAATGACGAACCTAGCAAGTGGTGAACTTG
CTTTTTGAAGAGACAGTTCATGAACAAGATACTCTTGGTACCGGAACAG

Alignment

ORF - retro_etel_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
          .PAYHSS..D.DT.LIGNMALLPIRSQFKG..P.ETKDT.IV.EAI..FK.NVFF.N.E.KNEADRT.I.
Retrocopy IPAYHSSIIDWDTNLIGNMALLPIRSQFKG*VPQETKDTYIVHEAIF*FKVNVFFQNIEMKNEADRTFIC

Parental  ITLYISECLKKLQKCNSR-SQGEKEM-YTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQ
          IT.Y.SECL.KLQKCNS..SQGEKE..YTLGIT.F.IP..P.FPLN.IYAKP..KQED..M.AYL..L.Q
Retrocopy ITPYSSECLRKLQKCNSK<SQGEKEV<YTLGITTFLIPRKPRFPLNVIYAKPESKQEDD-MKAYL*HLSQ

Parental  ETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
          ETGLRL.EK.FDPQND.PSKW.TCF.KRQFMNK.L..P.Q
Retrocopy ETGLRLREKIFDPQNDEPSKW*TCFLKRQFMNKILLVPEQ

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1323 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
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,
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,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
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,