RetrogeneDB ID: retro_etel_1860

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_308774:20067..20570(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSETEG00000013104
• Aliases: None
• Description: cysteine and histidine-rich domain (CHORD) containing 1 [Source:HGNC Symbol;Acc:14525]

Sequence

>retro_etel_1860
ACCTATCAGGGCTTAGAAATTCTAGAAGAAGTCTGTGTATATCATTCTGGAGTACCTATTTTCCATGAAGGGATGAAATA
CTGGAGCTGTTGTAGAAAAAAGATTTCTGAATTTAACACATTTAGCCCAAGAAGGCTGTACTACAGGGAAACACATGTGG
ACTTAAAAAAGATGCTGGGGGAAAAGTTGTTCCATGTAGGCATGACTGGCATCAGACGGGAGGTGAAGTCACCATTTCAA
TCTATGCTAAAAATTCACTTCCAGAATGTAGTCAAGTAGAAGCAAATAGTACATTGTTAAATGTTCTCATTGTATTTGAA
GGAGAGAAGGAATTCCATCAAAATGTGAAATTATGGGGCATGATTGACGTAAAGCGAAGCTATGTAACTATGACTGCAAC
AGAAATTGAGATCACCATGAGAAAAGCTGAACCTATGCAGTGGGCAAGCCTTGAACTACCTATCGCTAAAAAGCCAGAAA
AACAAAAAGAAGCTATAACAGAT

Alignment

ORF - retro_etel_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TYQGLESLEEVCVYHSGVPIFHEGMKYWSCCRKKTSDFNT-LAQEGCTTGKHMWT-KKDAGGKVVPCRHD
          TYQGLE.LEEVCVYHSGVPIFHEGMKYWSCCRKK.S.FNT.LAQEGCTTGKHMWT.KKDAGGKVVPCRHD
Retrocopy TYQGLEILEEVCVYHSGVPIFHEGMKYWSCCRKKISEFNT>LAQEGCTTGKHMWT>KKDAGGKVVPCRHD

Parental  WHQTGGEVTISIYAKNSLPERSRVEANSTLLNVLIVFEGEKEFHQNVKLWGVIDVKRSYVTMTATKIEIT
          WHQTGGEVTISIYAKNSLPE.S.VEANSTLLNVLIVFEGEKEFHQNVKLWG.IDVKRSYVTMTAT.IEIT
Retrocopy WHQTGGEVTISIYAKNSLPECSQVEANSTLLNVLIVFEGEKEFHQNVKLWGMIDVKRSYVTMTATEIEIT

Parental  MRKAEPMQWASLELPAVKKPENQEEAIAD
          MRKAEPMQWASLELP..KKPE.Q.EAI.D
Retrocopy MRKAEPMQWASLELPIAKKPEKQKEAITD

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_1860 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860 ,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,