RetrogeneDB ID: retro_etel_1299

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_243974:5599..6066(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSETEG00000015647
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_etel_1299
TCATATAGAGGAGCTGACCATGCAATTCGAGAGACAACCAGCATCCAGCGGATGAGAAGTTGCAGAAGAAGACATGGAAT
GCGGTGGTCCCACTAGCAGGTAAATTAAAGACATTTTATTAATTTCTCAGAGGTTAGAAGCAGCATTATAAGGTCTACTG
GGAGCCCCGACAAGCCCAGAGGGAAAGCAGGCTCTTGCTAATCAGTTTGCAGAAATCCTTCGTTTCACACTCTGGCTTGA
TGAACTCCAGATGGCAAATACTGCCATGCAGAATGATGTCGGTCTTACAGAAGAGCGTTGGGTCTTATGGGGATGAGCCA
CGTGTCCGCAGAAGGAGAGAATGAAGTCAATAATGAGTGGGCAAACTGAAGGTCTCTGTTTTATGCCGAAGCAACCCTGA
TGCTGGAGTCTTCAAGAGACACCACAACAAGCAGTGTGTCGAGAATACAAAGTGACCAGCAGAAGAT

Alignment

ORF - retro_etel_1299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SYRGAGHEIREAI-QHPADEKLQEKAWGAVVPLVGKLKKFYEF-SQRLESALRGLLGALTSTPYSPTQHL
          SYRGA.H.IRE...QHPADEKLQ.K.W.AVVPL.GKLK.FY.F.SQRLE.AL.G....L...P.SP....
Retrocopy SYRGADHAIRETT<QHPADEKLQKKTWNAVVPLAGKLKTFY*F<SQRLEAAL*G----LLGAPTSP----

Parental  EREQALAKQFAEILHFTLRFDELKMTNPAIQNDFSY-YRRTLSRMRINNVPAEGENEVNNELANRMSLFY
          E..QALA.QFAEIL.FTL..DEL.M.N.A.QND....YRR.L..M....V.AEGENEVNNE.AN..SLFY
Retrocopy EGKQALANQFAEILRFTLWLDELQMANTAMQNDVGL<YRRALGLMGMSHVSAEGENEVNNEWAN*RSLFY

Parental  AEATPMLKTLSDATTKFVS-ENKNLPIEN
          AEAT.ML....D.TT..VS.EN...P.E.
Retrocopy AEATLMLESSRDTTTSSVS<ENTK*PAED

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_1299 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299 ,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,