RetrogeneDB ID: retro_etel_68

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_1148:93833..94673(+)
• Located in intron of: ENSETEG00000014404

Retrocopy information

• Ensembl ID: ENSETEG00000014405
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000001796
• Aliases: None
• Description: None

Sequence

>retro_etel_68
GCGGCATTGGAACCTTCCATGGGAAAAGTATTCAAAATTGATCAGATGGGAAGAAGGTTTGTGGCTGGAGGAGCTGCGGT
TGGTCTTGGAGCATTGTGCTATTATGGCTTAGGGATGTCTAGTGAGATGGGAGCTATTGAAAAAGCTGTAATTTGGCCTC
AGTATGTGAAAGATAGAATTCACTCTCCTGATAGGTACCTAGCTGGAAGTATTGGTTTAACTGCCCTGTCAGCCATGGCC
GGGACTAGAACTCCTGTTCTCTTGAGTTTCATGTTGAGAGCTTCTTGGGTGACAATTGGTGCCACCTTTGCAGCCGTGAT
TGGCGCGGAATGCTGGTGCGGTCAATATCCTATGACCAGAGCCCGGGCCCAAAGCATCTGGCTTGGTTACGACATTGTGC
TGTGATGGGAGCAGTGGTGACGCCTCTGGCTGTATTAGGGGGACCTCTTCTCATCAGAGCTGCATGGTGTACAGCCGGCA
TCTTTGGGGGCCTCCCCACGGTGGCCATGTGTGCCCCCAGTGAGAAGTTTCTGAACAAGGGCGCACCCCTGGGAGCGGGC
CTTGGGCTCGGCTTTGTGTCCTCACTGGGATCTGTTTCTTCCACCCACCACTGTGGCCGGTGCCTCTCTGTATTCAGTAG
CGATGTATGGTGGATTCGTTCTTTTCAGCATGTTCCTTCTGTATGATGCACAGAAAGGAATCAAGCGTGCAGAAATAGCA
CCGATGTATGGCATTCAGAAATATGCTCCCATCAACGTGATGATGGGAGTCTACATGGACACATTAAACATATTTATGTG
AGTGGCCAGTACGCTAGCAACTGGAAGCAACAGAAGGAGA

Alignment

ORF - retro_etel_68 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 81.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAMEPSMEKVFKIDQMGRWFVAGGAAVGLGALCYYGLGMSSEMGAIEKAVIWPQYVKDRIHSTYMYLAGS
          AA.EPSM.KVFKIDQMGR.FVAGGAAVGLGALCYYGLGMSSEMGAIEKAVIWPQYVKDRIHS...YLAGS
Retrocopy AALEPSMGKVFKIDQMGRRFVAGGAAVGLGALCYYGLGMSSEMGAIEKAVIWPQYVKDRIHSPDRYLAGS

Parental  IGLTALSAMAVTRTPVLMSFMLRGSWVTIGATFAAMIGA-GMLVRSISYDQSPGPKHLAWLLHSGVMGAV
          IGLTALSAMA.TRTPVL.SFMLR.SWVTIGATFAA.IGA.GMLVRSISYDQSPGPKHLAWL.H..VMGAV
Retrocopy IGLTALSAMAGTRTPVLLSFMLRASWVTIGATFAAVIGA<GMLVRSISYDQSPGPKHLAWLRHCAVMGAV

Parental  VAPLAILGGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGLVFASSLGSM-FLPP-TTVA
          V.PLA.LGGPLLIRAAW.TAGI.GGL.TVAMCAPSEKFLN.GAPLG.GLGL.F.SSLGS..F..P.TTVA
Retrocopy VTPLAVLGGPLLIRAAWCTAGIFGGLPTVAMCAPSEKFLNKGAPLGAGLGLGFVSSLGSV<FFHP<TTVA

Parental  GATLYSVAIYGGLVLFSMFLLYDTQKVIKRAEIAPMYGIQKYDPINAMMGIYMDTLNIFMRVATMLATGS
          GA.LYSVA.YGG.VLFSMFLLYD.QK.IKRAEIAPMYGIQKY.PIN.MMG.YMDTLNIFM.VA..LATGS
Retrocopy GASLYSVAMYGGFVLFSMFLLYDAQKGIKRAEIAPMYGIQKYAPINVMMGVYMDTLNIFM*VASTLATGS

Parental  NRKK
          NR..
Retrocopy NRRR

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_68 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.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68 ,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,