RetrogeneDB ID: retro_etel_1671

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_286723:8909..9300(+)
• Located in intron of: ENSETEG00000011333

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMGT1
• Ensembl ID: ENSETEG00000005810
• Aliases: None
• Description: membrane magnesium transporter 1 [Source:HGNC Symbol;Acc:28100]

Sequence

>retro_etel_1671
ATGGCGCCGCTGCTGTGGAAGGGGGTGCTGGCCATGGGCCTCTTTGCCCTCGCCCACGCAGCGTTTTCGGCCACGCAGCA
TCGTTCTTATATGCGACTAACAGAAAAGGAAGACGAATCACTGCCAATCGACATAGTTCTTCAAACACTTCTGGCCTTTG
CGGTTACCTGTTGTGGTATTGTTCCTATGGCTGGGGAGTTTAAAGACATGGATGCTACATCAGAACTTAAAAAGAAGACA
TTTGATACACTGAGGAATCACCCATCGTTTTAGTGTGTTTAATCACCGTGGGCGAGTATTGTTCCGGCCTCCGGATTCAA
CAAACTTTTCAAAGCAAGATGGAATCTCCTCTTTGAACACATCATTGAAGTTCAGAAAATTTGACTCACTA

Alignment

ORF - retro_etel_1671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSLWKGVVGIGLFALVHAAFSAAQHRXXXXXXXXXXXSLPIDIVLQTLLAFAVTCYGIVHIAGEFKDM
          MAP.LWKGV...GLFAL.HAAFSA.QHR...........SLPIDIVLQTLLAFAVTC.GIV..AGEFKDM
Retrocopy MAPLLWKGVLAMGLFALAHAAFSATQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCCGIVPMAGEFKDM

Parental  DATSDLKNKTIDTLRNHPS-FYVFNHRGRVLFRPSDSANSSNQDALSS-NSSLKLRKLDSL
          DATS.LK.KT.DTLRNHPS.F.VFNHRGRVLFRP.DS.N.S.QD..SS.N.SLK.RK.DSL
Retrocopy DATSELKKKTFDTLRNHPS>FSVFNHRGRVLFRPPDSTNFSKQDGISSLNTSLKFRKFDSL

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_1671 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671 ,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,