RetrogeneDB ID: retro_etel_1005

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_199645:2918..3381(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAMTOR1
• Ensembl ID: ENSETEG00000010979
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 [Source:HGNC Symbol;Acc:26068]

Sequence

>retro_etel_1005
ATAGGGTGCTGCTGCAGCAGCGAGGAGAACTCTGACCAGGACCGAGAGGAACGGAAGCTGATGCTGGACCCTGGCAGTCC
TCCCACCAAAGCCCTCAATGGAGCTGACTGAGCCCAAGGACCACAGCCTGCCTTCCGCACGCACAGATGAGCAGGCCCTG
CTCTCTTCCATCCTTGCCAGGACAGCCAGCACCATCGTCCGTGTGTCTGCTGCGGGCTCCCAGGGCCTGGAGCAGCAGGA
GTACATGGACCGGGCAAGGCAGTACGGCGCCGTAGCAGCCTGACTGACCCCTTGGAAGAAGCTGCCATCTCTCACCAGCC
AGCACCACCCAGTGCTGGCCAGCGAGCCCATCCTATTCTCCGACTTGCCGCAGGTCCCCAGCATAGCTGCTTATGCCTAC
AGTGCGCTTCCTCAGATCCGTGTGAATGCAAAAGAGGAGCTCCTTGTACAGTTTGGGATCCCA

Alignment

ORF - retro_etel_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCCYSSENEDSDQDREERKLLLDPSSP-PTKALNGAEPNYHSLPSARTDEQALLSSILAKTASTIIDVS
          .GCC.SSE........E....L...S.P.P.......EP..HSLPSARTDEQALLSSILA.TASTI..VS
Retrocopy IGCCCSSEENSDQDREERKLMLDPGSPP>PKPSMELTEPKDHSLPSARTDEQALLSSILARTASTIVRVS

Parental  AADSQGMEQQKDMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYA
          AA.SQG.EQQ..MDRARQY..........LT.WKKLP...SLTSQ.H.VLASEPI.FSDL.QV..IAAYA
Retrocopy AAGSQGLEQQEYMDRARQY----GAVAA*LTPWKKLP---SLTSQHHPVLASEPILFSDLPQVPSIAAYA

Parental  YSALSQIRVDAKEELVVQFGIP
          YSAL.QIRV.AKEEL.VQFGIP
Retrocopy YSALPQIRVNAKEELLVQFGIP

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_1005 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436,
Canis familiaris	ENSCAFG00000005788	1 retrocopy	retro_cfam_1962,
Echinops telfairi	ENSETEG00000010979	1 retrocopy	retro_etel_1005 ,
Felis catus	ENSFCAG00000005320	2 retrocopies	retro_fcat_142, retro_fcat_496,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Myotis lucifugus	ENSMLUG00000014117	1 retrocopy	retro_mluc_2372,
Mustela putorius furo	ENSMPUG00000010289	3 retrocopies	retro_mputfur_1178, retro_mputfur_270, retro_mputfur_455,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,