RetrogeneDB ID: retro_etel_1160

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_219602:5819..6311(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009706
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000015365
• Aliases: None
• Description: None

Sequence

>retro_etel_1160
ATAGCAGGACAGATGACAAGGCATCTGCTGTTTCTCTTGCTGTTGGTGGCTGATGGATGGGGTATCATGAGCCAGGCTAC
ACCGGCCAGGACTGAACTCCTCAGTGTCTGCATGGATGCCAAGCACCACAAGGAAAAGCCAGGCCCTGATCACTCGTTGC
ACGACCAGTGTAGCCCCTGTAAGAAGAATGCCTGCTGCTCCAACAACAACCAGCCAGGAAGTCCACAAGAGCCTTTCCTA
CCTGGACAGATTCAACTGGGACCACAACGAGAAGATGCAGCCTGCCTGTGAGCGCCACTTCATCCAGGACGCCTGCTTCT
ATGAGTGCTCCCCAAACTTGGGACCCTGGATCCAACAGGTGGACCAGAGCTGATGCAAAGAGAGGGTGCTGAACGTGTCC
CTGTGCCAAGAGGACCGTCAGAGATGGTGGGAGGATTGCCACTCGTCTTATACCTGCAAGACCAACTGGCACAGGGCTGG
AACTGGACTTCA

Alignment

ORF - retro_etel_1160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.33 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGQVTMQLLFLLLLVADGWGIMRQSRPARTELLNVCMDAKHHKEKPGPEDKLHDQCTPWKKNACCSVN-
          .AGQ.T..LLFLLLLVADGWGIM.Q..PARTELL.VCMDAKHHKEKPGP...LHDQC.P.KKNACCS.N.
Retrocopy IAGQMTRHLLFLLLLVADGWGIMSQATPARTELLSVCMDAKHHKEKPGPDHSLHDQCSPCKKNACCSNN>

Parental  TSQEAHKDVSYLYRFNWDHCGKMQPACKRHFIQDTCFYECSPNLGPWIQQVDQSWRKERVLNVPLCQEDC
          TSQE.HK..SYL.RFNWDH..KMQPAC.RHFIQD.CFYECSPNLGPWIQQVDQS..KERVLNV.LCQED.
Retrocopy TSQEVHKSLSYLDRFNWDHNEKMQPACERHFIQDACFYECSPNLGPWIQQVDQS*CKERVLNVSLCQEDR

Parental  QMWWEDCRSSYTCKTNWHK-GWNWTS
          Q.WWEDC.SSYTCKTNWH..GWNWTS
Retrocopy QRWWEDCHSSYTCKTNWHR<GWNWTS

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_1160 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160 , retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,