RetrogeneDB ID: retro_etel_999

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_198829:4181..4783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARF
• Ensembl ID: ENSETEG00000009329
• Aliases: None
• Description: nuclear prelamin A recognition factor [Source:HGNC Symbol;Acc:29916]

Sequence

>retro_etel_999
TCAGGTGAGCTCCTGCAGATGGTGAAGCAGAGTGACCTCACCATGCAGGCAGCGGCTGTGAGCACTTTGTCTGAGACTTG
AGTGGGGAAGAGGCCCAGCGCCGTGAGGTAGCCGGCTCAGATGGGTACCTGGCCACATCTTCTGCAACGTTGCCAAGGAG
CGTGGCGAGGATATTGGGGAGAAGGTCACATATCGAGCCCTGAGAAACAGAGCTTCTGGGGGGCCACCCTGGAGAGAGAC
CGGGGAGGTGCTGCTCTGCGTGGCTGCTGCCTGCGTGGCTTCTGAAACGTCCAGACGCGGTCCTGGCGATGGAGACGGGC
AGGCCCCTGTACCAACTGGTGGAGGTCCTCGGTGTCCCAGAGGGCACATGCATGGCAGAGGCCAGGCCCCGGCTGAGGGT
GGTCCTGCAGACGAGGCATTGCTGGGGTAGATGGAAGACATCTCTGCGGAGGTCCCCACTCAGGCCCCCCAGGCCAGCGC
ACAGGTGCAGATGTTCCACCAGGACTGACTCCACCCCTCACCCCGCCCCCAGGGTGCAGACAACTCTGCAAACTGCTTTC
CCCAGCGCTGGGCTCGCCGCCGGTGCCTCAGACTTCAAGTGG

Alignment

ORF - retro_etel_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 53.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SGELLQMMEQSDLTVKDAAVDTLFR-DLTEEEIQRHEGAGSDGYLA-HVFRHAAKELFGEDV-EKVTYRA
          SGELLQM..QSDLT...AAV.TL...DL..EE.QR.E.AGSDGYLA.H.F...AKE..GED..EKVTYRA
Retrocopy SGELLQMVKQSDLTMQAAAVSTLSE<DLSGEEAQRREVAGSDGYLA<HIFCNVAKER-GEDIGEKVTYRA

Parental  LRNR-DFQEVTLEKD-GEVVLRFAAAYGFRNVQ-NVVLKLKKGRLPYHFVEVLA-CPGGCLHGRGQARAE
          LRNR..F...TLE.D.G...LR.....GF.NVQ...VL....GR..Y..VEVL..CP.G..HGRGQA.AE
Retrocopy LRNR<SFWGATLERDRGGAALRGCCLRGF*NVQ<DAVLAMETGRPLYQLVEVLG<CPRGHMHGRGQAPAE

Parental  DGPADKVLLQQMEDIYAEVPTRPPEASAQVRTLYQEWLHGA-DPPRVQEALHTSFPSAGLAASSLDIKW
          .GPAD..LL..MEDI.AEVPT..P.ASAQV....Q..LH.....PRVQ..L.T.FPSAGLAA...D.KW
Retrocopy GGPADEALLG*MEDISAEVPTQAPQASAQVQMFHQD*LHPS>PAPRVQTTLQTAFPSAGLAAGASDFKW

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_999 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018178	1 retrocopy	retro_btau_820,
Canis familiaris	ENSCAFG00000012976	1 retrocopy	retro_cfam_659,
Dasypus novemcinctus	ENSDNOG00000011246	1 retrocopy	retro_dnov_1757,
Echinops telfairi	ENSETEG00000009329	1 retrocopy	retro_etel_999 ,
Myotis lucifugus	ENSMLUG00000017740	23 retrocopies	retro_mluc_1006, retro_mluc_1012, retro_mluc_1083, retro_mluc_1091, retro_mluc_1124, retro_mluc_1256, retro_mluc_1282, retro_mluc_1457, retro_mluc_1573, retro_mluc_1622, retro_mluc_1632, retro_mluc_1700, retro_mluc_1718, retro_mluc_1898, retro_mluc_1973, retro_mluc_2365, retro_mluc_671, retro_mluc_688, retro_mluc_817, retro_mluc_825, retro_mluc_877, retro_mluc_879, retro_mluc_982,