RetrogeneDB ID: retro_etel_297

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4893:243669..245033(-)
• Located in intron of: ENSETEG00000017364

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSETEG00000017166
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_etel_297
ATGTCTCACCTGCCGATGAAACTCCTGCGCAAGAAGATCGAGAAGCGGAATCAGAAATTGCCGCAACGAAACCTAAAGCT
ACAGGGGCAGCAGGTGTGAGCATATCAGAAGGGCAGAATGGAGATGTGCCACAACCAACAGTGGGAGATGAAAAAGATAG
AAAATCCTTAAAACCGTCTATGAAGATGGGCTTCTCAGGACCCCAAAATGGAAATGTGTCTAAAGAAACAGTGGAAAATG
TAAAAATTAAAAACTCTCCCAAGAAACCTGCTGTTTCATCCAATGGGGAAGCAACAACACAAGCTCCTAATGCAAAATTG
AAAAAGAAGAAGAAGAAAAGGAAAATGGAGGGTGCTGCCAGGCCTGATATAAAAAAGACAAAAACTGAAGACACCGAGGA
GACTAAAAAGTGTGACATCCAGACTCCGGCAGAAGCAGAAACAAGAATGGAACAGCCAGATGGTGACGAAGAGGATAGTG
AATTGCCCAGCCTGCCCCTGGGACTGACGGGTGCTTTTGAAGATACTTCATTTACTTCACTGGCTAATCTTGTCAATGAA
AGCACTCTGAAGTCCATTAAAGAAATGGGCTTTACAAATATGACTGAAATTCAGCATAAAAGTATCAGACCACTTCTGGA
AGGCAGGGATCTTCTGGCAGCTGCGAAAATAGGCAGTGGTAAAACGCTCGCGTTTCTCATCCCTGCAGTTGAACTCATTG
TTAAGTTAAAATTCATGCCCAGGAACGGAACAGGAGTTCTTATTCTCTCCCCCACTAGGGAACTGGCCATGCAGACGTTT
GGTGTGCTGAAGGAGCTAATGACACACCATGTTCACACGTATGGGCTGATCATGGGGGGTAGTAACAGATCTGCGGAAGC
ACAGAAACTTGCTAACGGGATCAACATCGTTGTAGCTACACCAGGCCGCCTCCTGGACCATATGCAGAGTACTCCAGGGT
TTATGTATAAAAACCTACAGTGCCTGGTCATTGATGAAGCTGATCGTATCTTGGATGTTGGATTTGAAGAGGAGTTAAAG
CAGATTATTAAACTTCTGCCAGTACGCAGACAGACCATGCTTTTTTCTGCCACTCAAACTCGAAAGGTTGAAGACCTGGC
GAGGATTTCTCTGAAAAAGGAGCCTTTGTGTGGCGGTGTTGATGATGATAAAGCCAATGCAACTGTGGATGGTCTTGAGC
AGGGCTACGTTGTCTGTCCCTCTGAAAAAAGATTCCTTCTGCTGTTTACCTTCCTGAAGAAGAACCGAAAGAAGAAACTG
ATGGTGTTCTTTTCGTCCTGCATGTCTGTCAAATACCACTATGAGTTGCTGAACTACATTGACTTGCCTGTCTTGGCCAT
TCAT

Alignment

ORF - retro_etel_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 68.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNQKLRQRNLKLQG-AAGVSTSEGQNGDVPQPTVGDENERKSLKPSMKMGFSGPQ
          MSHLPMKLLRKKIEKRNQKL.QRNLKLQG.AAGVS.SEGQNGDVPQPTVGDE..RKSLKPSMKMGFSGPQ
Retrocopy MSHLPMKLLRKKIEKRNQKLPQRNLKLQG<AAGVSISEGQNGDVPQPTVGDEKDRKSLKPSMKMGFSGPQ

Parental  NGNVSKETVDNVKIKNSPKKPAVLSNGEAATQAPNSKLKKKKKKRKMEDAARPDIKKAKTEDTEESKKCD
          NGNVSKETV.NVKIKNSPKKPAV.SNGEA.TQAPN............E.AARPDIKK.KTEDTEE.KKCD
Retrocopy NGNVSKETVENVKIKNSPKKPAVSSNGEATTQAPNXXXXXXXXXXXXEGAARPDIKKTKTEDTEETKKCD

Parental  IQTPAEAETRMEQPDGDEEDNELPSLPLGLTGAFEDTSFTSLANLVNENTLKSIKEMGFTNMTEIQHKSI
          IQTPAEAETRMEQPDGDEED.ELPSLPLGLTGAFEDTSFTSLANLVNE.TLKSIKEMGFTNMTEIQHKSI
Retrocopy IQTPAEAETRMEQPDGDEEDSELPSLPLGLTGAFEDTSFTSLANLVNESTLKSIKEMGFTNMTEIQHKSI

Parental  RPLLEGXXXXXXXXXXXXXXXXXXXPAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH
          RPLLEG...................PAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH
Retrocopy RPLLEGRDLLAAAKIGSGKTLAFLIPAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVH

Parental  TYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQI
          TYGLIMGGSNRSAEAQKLANGINI.VATPGRLLDHMQ.TPGFMYKNLQCLVIDEADRILDVGFEEELKQI
Retrocopy TYGLIMGGSNRSAEAQKLANGINIVVATPGRLLDHMQSTPGFMYKNLQCLVIDEADRILDVGFEEELKQI

Parental  IKLLPVRRQTMLFSATQTRKVDDLARISLKKEPLYVGVDGEGSNSESGVVGLENGYVVCPSEKRFLLLFT
          IKLLPVRRQTMLFSATQTRKV.DLARISLKKEPL..GVD....N....V.GLE.GYVVCPSEKRFLLLFT
Retrocopy IKLLPVRRQTMLFSATQTRKVEDLARISLKKEPLCGGVDDDKANAT--VDGLEQGYVVCPSEKRFLLLFT

Parental  FLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH
          FLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH
Retrocopy FLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH

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_297 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 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297 ,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,