RetrogeneDB ID: retro_etel_1919

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_314172:73364..74729(-)
• Located in intron of: None

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_1919
ATGTCTCACCTGCCGATGAAACTCCTGCGCAAGAAGATCGAGAAGCGGAATCAGAAATTGCGGCAACGAAACCTGAAGCT
ACAGGGGGCAGCAGGTGTGAGCATACCAGAAGGGCAGAATGGAGATGTGCCTCAACCAACAGTGGGAGATGAAAAAGATA
GAAAATCCTTAAAACCGTCCATGAAGATGGGCTTCTCAGGACCCCAAAATGGAAATGTGTCTAAAGAAACGGTGGACAAT
GTAAAAATTAAAAACTCCCCCAAGAAACCTGCTGTTTTATCCAATGGGGAAGCAGCAACACAAGCTCCTAATTCAAAATT
GAAAAAAAAGAAGAAGAAAAGGAAAATGGAGGATGCTGCCAGGCCTGATATAAAAAAGGCAAAAACTGAAGACACCGAGG
AGTCTAAAAAGTGTGACATCCAGACTCCGGCAGAAGCAGAAACAAGAATGGAACAGCCAGATGGTGACGACGAGGATAAT
GAATTGCCCAGCCTGCCCCTGGGACTGACAGGTGCTTTTGAAGATACTTCATTTACTTCACTGGCTAATCTTGTCAATGA
AAACACTCTGAAGTCCATTAAATAAATGGGCTTTACAAATATGACTGAAATTCAGCATAAAAGTATCAGACCACTTCTGG
AAGGCAGGGATCTCCTGGCAGCTGCGAAAACAGGCAGTGGTAAAACGCTCGCGTTTCTCATCCCTGCAGTTGAACTCATT
GTTAAGTTAAAATTCATGCCCAGGAACGGAACAGGAGTTCTTATTCTCTCCCCCACTAGGGAACTGGCCATGCAGACGTT
TGGTGTGCTGAAGGAGCTAATGACACACCATGTTCACACGTATGGGCTGATCATGGGGGGTAGTAACAGATCTGCGGAAG
CACAGAAACTTGCTAACGGGATCAACATCGTTGTAGCTACACCAGGCCGCCTCCTGGATCATATGCAGAATACTCCAGGG
TTTATGTATAAAAACCTACAGTGCCTGGTCATTGATGAAGCTGATCATATCTTGGATGTTGGATTTGAAGAGGAGTTAAA
GCAGATTATTAAACTTCTGCCAGTACGCAGACAGACCATGCTTTTTTCTGCCACTCAAACTCGAAAGGTTGAAGACCTGG
CAAGGATTTCTCTGAAAAAGGAGCCTTTGTATGTCGGCGTCGATGATGATAAAGCCAATGCAACCGTGGATGGTCTTGAG
CAGGGCTACGTTGTCTGTCCCTCTGAAAAAAGATTCCTTCTGCTCTTTACCTTCCTGAAGAAGAACCGAAAGAAGAAACT
GATGGTGTTCTTTTCATCCTGCATGTCTGTCAAATACCACTATGAGTTGCTGAACTACATTGACTTGCCTGTCTTGGCCA
TTCAT

Alignment

ORF - retro_etel_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 68.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHLPMKLLRKKIEKRNQKLRQRNLKLQGAAGVSTSEGQNGDVPQPTVGDENERKSLKPSMKMGFSGPQN
          MSHLPMKLLRKKIEKRNQKLRQRNLKLQGAAGVS..EGQNGDVPQPTVGDE..RKSLKPSMKMGFSGPQN
Retrocopy MSHLPMKLLRKKIEKRNQKLRQRNLKLQGAAGVSIPEGQNGDVPQPTVGDEKDRKSLKPSMKMGFSGPQN

Parental  GNVSKETVDNVKIKNSPKKPAVLSNGEAATQAPNSKLKKKKKKRKMEDAARPDIKKAKTEDTEESKKCDI
          GNVSKETVDNVKIKNSPKKPAVLSNGEAATQAPNSKL.........EDAARPDIKKAKTEDTEESKKCDI
Retrocopy GNVSKETVDNVKIKNSPKKPAVLSNGEAATQAPNSKLXXXXXXXXXEDAARPDIKKAKTEDTEESKKCDI

Parental  QTPAEAETRMEQPDGDEEDNELPSLPLGLTGAFEDTSFTSLANLVNENTLKSIKEMGFTNMTEIQHKSIR
          QTPAEAETRMEQPDGD.EDNELPSLPLGLTGAFEDTSFTSLANLVNENTLKSIK.MGFTNMTEIQHKSIR
Retrocopy QTPAEAETRMEQPDGDDEDNELPSLPLGLTGAFEDTSFTSLANLVNENTLKSIK*MGFTNMTEIQHKSIR

Parental  PLLEGXXXXXXXXXXXXXXXXXXXPAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHT
          PLLEG...................PAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHT
Retrocopy PLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHT

Parental  YGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQII
          YGLIMGGSNRSAEAQKLANGINI.VATPGRLLDHMQNTPGFMYKNLQCLVIDEAD.ILDVGFEEELKQII
Retrocopy YGLIMGGSNRSAEAQKLANGINIVVATPGRLLDHMQNTPGFMYKNLQCLVIDEADHILDVGFEEELKQII

Parental  KLLPVRRQTMLFSATQTRKVDDLARISLKKEPLYVGVDGEGSNSESGVVGLENGYVVCPSEKRFLLLFTF
          KLLPVRRQTMLFSATQTRKV.DLARISLKKEPLYVGVD....N....V.GLE.GYVVCPSEKRFLLLFTF
Retrocopy KLLPVRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANAT--VDGLEQGYVVCPSEKRFLLLFTF

Parental  LKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH
          LKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH
Retrocopy LKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIH

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_1919 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,