RetrogeneDB ID: retro_etel_399

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_6749:9695..9979(+)
• Located in intron of: ENSETEG00000008749

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUTF2
• Ensembl ID: ENSETEG00000016354
• Aliases: None
• Description: nuclear transport factor 2 [Source:HGNC Symbol;Acc:13722]

Sequence

>retro_etel_399
ATTGACATGTCATGCCTTACATGGGAAGGACAGAAGTTGCAGGAGAAAGCATCCATTGTGCAGAAGTTGTCTAGCCTTCC
ATTCCAGAAAATCCAGCACAGCATCACGTCGCAGGACCATCAGCCCACGCCAGATGGCTGCCTCCTCAGCATGGGTGAGG
GCCAGCTGAAGGCTGATAAAGACCCCATCATGGGCTTTCACCAGTTGTTTCCTACTAACAAATATCAACGATGCCTGGGT
TTGCACAAGTGACATGGTCAGATCTTACTCTGCACCACTTGGGC

Alignment

ORF - retro_etel_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITSQDHQPTPDSCILSMVVGQLKADEDPIMGFHQM-
          ID.SCLTWEGQ..Q.KA.IV.KLSSLPFQKIQHSITSQDHQPTPD.C.LSM..GQLKAD.DPIMGFHQ..
Retrocopy IDMSCLTWEGQKLQEKASIVQKLSSLPFQKIQHSITSQDHQPTPDGCLLSMGEGQLKADKDPIMGFHQL>

Parental  FLLKNINDAWVCTNDMFR-LALHNFG
          FLL.NINDAWVCT.DM.R.L.LH..G
Retrocopy FLLTNINDAWVCTSDMVR>LTLHHLG

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_399 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 22 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Choloepus hoffmanni	ENSCHOG00000003059	3 retrocopies	retro_chof_1386, retro_chof_1619, retro_chof_2488,
Equus caballus	ENSECAG00000021530	1 retrocopy	retro_ecab_151,
Echinops telfairi	ENSETEG00000016354	9 retrocopies	retro_etel_1700, retro_etel_1737, retro_etel_1909, retro_etel_1925, retro_etel_245, retro_etel_281, retro_etel_301, retro_etel_399 , retro_etel_746,
Felis catus	ENSFCAG00000008167	3 retrocopies	retro_fcat_154, retro_fcat_743, retro_fcat_845,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mustela putorius furo	ENSMPUG00000006737	4 retrocopies	retro_mputfur_229, retro_mputfur_614, retro_mputfur_714, retro_mputfur_962,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Ochotona princeps	ENSOPRG00000013727	4 retrocopies	retro_opri_1089, retro_opri_1102, retro_opri_1170, retro_opri_229,
Procavia capensis	ENSPCAG00000015344	1 retrocopy	retro_pcap_56,
Pteropus vampyrus	ENSPVAG00000016605	1 retrocopy	retro_pvam_843,
Sorex araneus	ENSSARG00000007472	1 retrocopy	retro_sara_333,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Tupaia belangeri	ENSTBEG00000011016	1 retrocopy	retro_tbel_7,
Tarsius syrichta	ENSTSYG00000010702	3 retrocopies	retro_tsyr_1689, retro_tsyr_380, retro_tsyr_745,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,