RetrogeneDB ID: retro_etel_1573

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279523:57704..58551(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004633
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000006890
• Aliases: None
• Description: None

Sequence

>retro_etel_1573
GGGAATGACACCAAGAAGTTAAAGGTGACAGCCGGAGCTTGGATGCCCCTTCTCGCGTGGTCCATGTCTGCAAGCTGCCA
GGTGATGTCACCTAGGGGGAGGTCATCTCCCTGGGACTGCCCTTCAGGGAGGTGACCAACCTGCTGATGCTGAAGGTGAA
GAACCAGGCCTTCACCGAGATGAACACGGAGGAGGCGACCAACACCATGGTGAATTACTACACCTCGGTGGCTGCCATGC
TGCATGGGCAGCCCATCTACATCCAGTTCTCCAACCATAAGGAGCTCAAGACGGACGGCTCTCCCAACCACGTGCGCGCC
TAGGCTGCCCTGCAGGCCATCAACTTGGTGCAGTCCGGGAGCCTGGCACTGGCGGCCTCCCGCTGCCGCCGTGGACGCAA
GGATGTCTGTGGCGGGCCAGAGCCCCGTGCTGCGGGTCACTGTAGAGAACTTATTCTACCCGGTGACACTGGATGTGCTG
CACCAGATCTTCTCCAAGTTTGGCACGGTGCTCAAAATCGTCACCTTCACCAAGAACAACCAGTTCCAGGCGCTTCTGCA
GTATGCCTAACCTGTCAGCGCCCAGCACGCCAAGCTGTCCCTGCACGGCCAGAACATCTACAATGCTTGCTGCACGCTGC
GCATTGACTTCTCGAAGCTCACCAGCCTCAACGTCATGTACAACAACGAAAAGAGCCGAGACTACTCTCGGCCGACCTGC
CCTCGGGGGACAGCAGCCATCTCCGGACCAGACCATGGCTGCGGCCTTTGGTGCACCTGGTATAATCTCAGCCTCACCGT
ACGCAGGAGCCGGGTTCCCTCCCACCTTCGCCATCCCACAGGCCGCA

Alignment

ORF - retro_etel_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.2 %
• Parental protein coverage: 54.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GNDTKKFK-GDSRSSGAPSRVVHVRKLPGDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANT
          GNDTKK.K.GDSRS..APSRVVHV.KLPGDVT.GEVISLGLPF..VTNLLMLK.KNQAF.EMNTEEA.NT
Retrocopy GNDTKKLK<GDSRSLDAPSRVVHVCKLPGDVT*GEVISLGLPFREVTNLLMLKVKNQAFTEMNTEEATNT

Parental  MVNYYASVAAMLRGQPIYIQFSNHKELKTDGSPNQARAQAALQAVNSVQSGSLALAAS-AAAVDAGMAVA
          MVNYY.SVAAML.GQPIYIQFSNHKELKTDGSPN..RA.AALQA.N.VQSGSLALAAS.AAAVDA.M.VA
Retrocopy MVNYYTSVAAMLHGQPIYIQFSNHKELKTDGSPNHVRA*AALQAINLVQSGSLALAAS>AAAVDARMSVA

Parental  GQSPVLRVIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYAEPVSAQHAKLSLDGQNIYN
          GQSPVLRV.VENLFYPVTLDVLHQIFSKFGTVLKI.TFTKNNQFQALLQYA.PVSAQHAKLSL.GQNIYN
Retrocopy GQSPVLRVTVENLFYPVTLDVLHQIFSKFGTVLKIVTFTKNNQFQALLQYA*PVSAQHAKLSLHGQNIYN

Parental  ACCTLRIDFSKLTSLNVKYNNDKSRDYTRP-DLPSGDS-QPSLDQTMAAAFGAPGIISASPYAGAGFPPT
          ACCTLRIDFSKLTSLNV.YNN.KSRDY.RP.DLPSGDS.QPS.DQTMAAAFGAPGIISASPYAGAGFPPT
Retrocopy ACCTLRIDFSKLTSLNVMYNNEKSRDYSRP<DLPSGDS<QPSPDQTMAAAFGAPGIISASPYAGAGFPPT

Parental  FAIPQAA
          FAIPQAA
Retrocopy FAIPQAA

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_1573 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000003779	1 retrocopy	retro_etel_886,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573 ,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,