RetrogeneDB ID: retro_etel_1765

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_292570:157922..158179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSETEG00000001558
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_etel_1765
ATGAGTCTACCCCTCAATCCCAAACCTTCCCTGAACGACTAACAGGAAAGCCAGTGGTGGTGAAAGTGAAGAGGGACATG
GAGTACAGGGCTACCTGGTATCTGTAGATGGCCCTGTGAGCATGCAGCTTGCGAATACAGACGAATACATACATGGGACA
TTGTCTGGATATCTGGATGAAGTTTTAATAAGGTGTCATAATGGTTCTTTATATCAGAGGTGATGAAGTAGAGGAAGAAG
ATGGAGAAATGAGAGAG

Alignment

ORF - retro_etel_1765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNG-LTGKPVMVKLKWGMEYK-GYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNN
          MSLPLNPKP.LN..LTGKPV.VK.K..MEY..GYLVSVDG...MQLANT.EYI.G.LSG.L.EVLIRC.N
Retrocopy MSLPLNPKPSLND<LTGKPVVVKVKRDMEYR<GYLVSVDGPVSMQLANTDEYIHGTLSGYLDEVLIRCHN

Parental  -VLYIRGVEEEEEDGEMRE
          .VLYIRG.E.EEEDGEMRE
Retrocopy >VLYIRGDEVEEEDGEMRE

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_1765 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 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Echinops telfairi	ENSETEG00000001558	3 retrocopies	retro_etel_1765 , retro_etel_1846, retro_etel_560,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,