RetrogeneDB ID: retro_etel_11

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5078:78405..78960(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000015362
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSETEG00000000242
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_etel_11
ATGCGTGAATATAAGTTAGTCGTACTTGGCTCGGGAGGTGTTGGAAAGTCTGCTCTGACTGTACAGTTTGTTCAAGGAAT
TTTTGTTGAAAAATATGATCCTACGATAGAAGATTCTTACAGAAAGCAAGTTGAAGTAGATGCACAACAGTGTATGCTTG
AAATCTTGGATACTGCAGGAACGGAACAATTTACAGCAATGAGGGATTTGTACATGAAAAATGGACAAGGTTTTGCATTA
GTTTATTCCATCACAGCACAATCCACGTTTAATGATTTGCAAGATCTGAGAGAACAGATTCTTCGAGTTAAGGATACTGA
TGATGTTCCAATGATTCTGGTTGGTAATAAGTGTGACTTAGAAGACGAAAGAGTCGTAGGAAAGGAACAAGGTCAAAATC
TAGCACGACAGTGGAACAACTGTGCATTCTTAGAATCTTCTGCAAAGTCAAAAATAAATGTTAATGAGATCTTTTATGAC
CTAGTGCGGCAAATTAACAGAAAAACTCCTGTGCCTGGGAAGGCCCGCAAAAAGTCATCGTGTCAGCTGCTTTAA

Alignment

ORF - retro_etel_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
Retrocopy MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
          YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
Retrocopy YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN

Parental  CAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          CAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
Retrocopy CAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL

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_11 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 26 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Bos taurus	ENSBTAG00000008967	3 retrocopies	retro_btau_1564, retro_btau_297, retro_btau_684,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11 ,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Echinops telfairi	ENSETEG00000019899	2 retrocopies	retro_etel_1028, retro_etel_391,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tarsius syrichta	ENSTSYG00000000192	1 retrocopy	retro_tsyr_910,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,