RetrogeneDB ID: retro_etel_1548

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_277835:48658..49561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSETEG00000000096
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_etel_1548
GACAACACAGAGTTCAGAGACATCGTTATCTCAAGCAACATTATCCCACATCTACTAGCCCTGGCTTCAACAACCATACC
AATCACATTTCTGCGGAACATTGCGTGGACCCTTTCCAACCTGTGCCGGAACAAGGACCCTTGTGAAGAGGCAGTGAAGG
AAATGCTGCCTGCCCTCTTAAACCTCCTGCAACACGATGACATCGAGGTTCTCTCGGATGCCTGCTGGGCCCTGTCCTAC
CTCCCTGATGGCTGCCAGGAGCGCACGGACCAAGTGGTTGCCACGGGAGTTCTATCCAGGATGGTGGAGCTCAGGAAAAG
CTCAGAACTCTGTATCATGACCCCCTCTCTCCGCACGGTAAGAAATATCGTCACAGGAACAGATCAACAGACCCAGAAGG
CCATCGACGCGGGCATGCTGGATGTGCTGGTCCAGCACCTGAGGCACCCCAAGTCCTCCATCCAGAAGGAGGCGGCCTGG
ACACTGAGCAACGTGGCTGCAGGGAACTGCCAGCACACGGAGCAGCTGATCAAACCTGGCATGCTGCCCATCTTGGTGTC
GGTGCTGAGAAATGGAGAGTTTAAAGTCCAAAAAGAGGCTGGGTGGGTGGAGGCTAACTTCACGATGGGGAGCATCACGG
ATCAGTTGGCCATGCTCATCCAATCGGGAGTCCTGAAGCCCCTGACGAGTCTGCTCATTTGCCATGACCACAAGACCGTT
ATCATCGTCCTTCAGACCACCTTCTGTATTCTCCAGTTTGCAGTGAATTCTCACGATATGGAGAAGCTCCGTCTCACGCT
AGAACAACTGGGTACCATTGAGAAAATCGAGGCGTTACAACTTCATGAGAACCATCAGATTGGGCAGACTGCGTTCAACA
TCATCGAGAACCTTCTCACGAAG

Alignment

ORF - retro_etel_1548 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 62.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNTEFRDIVISSNIIPHLLALASTTIPITFLRNIAWTLSNLCRNKDPYPCEEAVKEMLPALLNLLQHDDV
          DNTEFRDIVISSNIIPHLLALASTTIPITFLRNIAWTLSNLCRNKDP..CEEAVKEMLPALLNLLQHDD.
Retrocopy DNTEFRDIVISSNIIPHLLALASTTIPITFLRNIAWTLSNLCRNKDP--CEEAVKEMLPALLNLLQHDDI

Parental  EVLSDACWALSYLTDGCQERIDQVVAAGVLPRMVELMKSSELRIMTPSLRTVGNIVTGTDQQTQKAIDAG
          EVLSDACWALSYL.DGCQER.DQVVA.GVL.RMVEL.KSSEL.IMTPSLRTV.NIVTGTDQQTQKAIDAG
Retrocopy EVLSDACWALSYLPDGCQERTDQVVATGVLSRMVELRKSSELCIMTPSLRTVRNIVTGTDQQTQKAIDAG

Parental  MLDVLVQLLRHPKSSIQKEAAWTLSNVAAGNCQHIEQLINHGMLPILVSLLRNGEFKVQKEAVWVVANFT
          MLDVLVQ.LRHPKSSIQKEAAWTLSNVAAGNCQH.EQLI..GMLPILVS.LRNGEFKVQKEA.WV.ANFT
Retrocopy MLDVLVQHLRHPKSSIQKEAAWTLSNVAAGNCQHTEQLIKPGMLPILVSVLRNGEFKVQKEAGWVEANFT

Parental  MGSTPDQLAMLIQSGVLKPLTSLLTCHDHKTVVIILQTIFYILQSAVKR--FEKFCLTLEQLGTIEKIEA
          MGS..DQLAMLIQSGVLKPLTSLL.CHDHKTV.I.LQT.F.ILQ.AV.....EK..LTLEQLGTIEKIEA
Retrocopy MGSITDQLAMLIQSGVLKPLTSLLICHDHKTVIIVLQTTFCILQFAVNSHDMEKLRLTLEQLGTIEKIEA

Parental  LQLHENHQIGQTAFNIIENLLTK
          LQLHENHQIGQTAFNIIENLLTK
Retrocopy LQLHENHQIGQTAFNIIENLLTK

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_1548 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 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548 ,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Echinops telfairi	ENSETEG00000019546	1 retrocopy	retro_etel_1695,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,