RetrogeneDB ID: retro_etel_1574

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_279603:5211..5730(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFDP1
• Ensembl ID: ENSETEG00000016429
• Aliases: None
• Description: craniofacial development protein 1 [Source:HGNC Symbol;Acc:1873]

Sequence

>retro_etel_1574
AAGGCACAGAAAACCAAAGAGACAAACAAAAAGGCTGCAGGCATTCGCACCAGGAAGAGAAAACAAGCGGGCCTGTCATC
AGAAGGAGGAGGAGGAGAGCTAGATCCTGCAGCAGAATCGGGAAGCAGCCGCAGTGCCGACATAGATGAAGGTGCAGAGC
CAGACAAGGGGCCTTGAGTCAGAGGATGCAAGAAAAAGAATGCAGATGAACTCCGGGCCGCTCGTGAATGATGTGGGACC
CAAATCAAGAGTGTCCCTGAGTCCAGGAGTTAAGCAAAGAGAGGAGGCTGAAAGAGACAAGTTCTAGAACGTTGTTGGTC
AAAGCAGAAGCATGGAGAAACCTAAGGAACTAAAAAGGTCAAAATCACCGAGGTGCTTGACTGTGCTGGGGAAGAAGTCG
GGGTGACTAAGGAGGTGGAGACTCCTTCTAAAGAGGCCAAATTCTTCCTCAAGCAAAATGAAAAAGAGGAGCGCCAGGCG
GACTGGCCTTCAGCGCTGCCCTCACTCCCTGCAGGGTCA

Alignment

ORF - retro_etel_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.04 %
• Parental protein coverage: 57.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QAQETKGTKRKAAGIPSRKRKQGGLSLEGEE-ELDAEAESGGSSSDEEDEGAEQEKG-IGSEDARKKEED
          .AQ.TK.T..KAAGI..RKRKQ.GLS.EG...ELD..AESG.S.S...DEGAE..KG...SEDARK....
Retrocopy KAQKTKETNKKAAGIRTRKRKQAGLSSEGGGGELDPAAESGSSRSADIDEGAEPDKG>LESEDARKRMQM

Parental  ELWASFLNDVGPKSKVPPSTQVKQGEEIE-ETSSSKLLVKAE-EMEKPKE-TEKVTITKVFDFAGEEVRV
          .......NDVGPKS.V..S..VKQ.EE.E.ETSS..LLVKAE..MEKPKE.T.KV.IT.V.D.AGEEV.V
Retrocopy NS-GPLVNDVGPKSRVSLSPGVKQREEAE>ETSSRTLLVKAE<SMEKPKE<TKKVKITEVLDCAGEEVGV

Parental  TKEVEATSKEAKSFFKQNENEKPQVNSPSALPSLPAGS
          TKEVE..SKEAK.F.KQNE.E..Q...PSALPSLPAGS
Retrocopy TKEVETPSKEAKFFLKQNEKEERQADWPSALPSLPAGS

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_1574 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000695	1 retrocopy	retro_cpor_465,
Dasypus novemcinctus	ENSDNOG00000013266	2 retrocopies	retro_dnov_2442, retro_dnov_2546,
Echinops telfairi	ENSETEG00000016429	1 retrocopy	retro_etel_1574 ,
Myotis lucifugus	ENSMLUG00000000890	1 retrocopy	retro_mluc_2525,
Rattus norvegicus	ENSRNOG00000019326	1 retrocopy	retro_rnor_2289,
Ictidomys tridecemlineatus	ENSSTOG00000004124	2 retrocopies	retro_itri_1117, retro_itri_1815,
Tupaia belangeri	ENSTBEG00000015362	2 retrocopies	retro_tbel_1305, retro_tbel_2189,
Tursiops truncatus	ENSTTRG00000001215	1 retrocopy	retro_ttru_1385,