RetrogeneDB ID: retro_etel_1296

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_243651:602..1133(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000016064
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRABD
• Ensembl ID: ENSETEG00000005772
• Aliases: None
• Description: TraB domain containing [Source:HGNC Symbol;Acc:28805]

Sequence

>retro_etel_1296
TTCAGTGAGGCCTTCAAAGAGGTCAGCAAGGTGCCCTTCTGCAAGTTCCACCTGGGCGGCCGCCCCATTCCCGTTACCTT
CAAGAGGGCCATCGCTGCACTGTCCTTCCGGCAGAAGATCAAGCTGGCCTGGGGCCTCTGCTTCCCGTCGTACCCCATCA
GCAAGGACGATGTGGAGAAGTGTAAGCAGAAGGGCCTGCTGGAGCGGATGATGGCCCAGATAATCCGCGAGTTCCCCGGC
TTTCACTGCACCGTCATGTCCGAGCGAGGCGTCCACCTGACCCTAAATGCTGCTCCAGGCTGCCCGCAGCTTGGAGCTGC
CCGGTTCCTCGGATGCCGAGCCCAGGAAGTGCGTCCCCTCTGTGGTGATGGGCGTTGTGGCATGGGCCACGTGCCAGGCA
TCCAGAAGAACTAGAGCACCGAGCTGAACATACAGGAGATCATGACTGTTCCCCCACCCTCCGTCTCCGGCCGTGTGTCC
TGGCTGGCGGTCAAGGCCGCCTTCTTCGGCGTCATGGGCTACAGCCTCCAC

Alignment

ORF - retro_etel_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 78.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FREAFKEASKVPFCKFHLGDRPIPVTFKRAIAALSFWQKVKLAWGLCFLSDPISKDDVEKCKQKDLLEQM
          F.EAFKE.SKVPFCKFHLG.RPIPVTFKRAIAALSF.QK.KLAWGLCF.S.PISKDDVEKCKQK.LLE.M
Retrocopy FSEAFKEVSKVPFCKFHLGGRPIPVTFKRAIAALSFRQKIKLAWGLCFPSYPISKDDVEKCKQKGLLERM

Parental  MAEMIGEFPDLHRTIVSERDIYLTY-MLRQAARRFELPGSSDAEPRKCVPSVVVGVV-GMGHVPGIEKNW
          MA..I.EFP..H.T..SER...LT..ML.QAAR..ELPGSSDAEPRKCVPSVV.GVV.GMGHVPGI.KN.
Retrocopy MAQIIREFPGFHCTVMSERGVHLTL>MLLQAARSLELPGSSDAEPRKCVPSVVMGVV<GMGHVPGIQKN*

Parental  STELNIQEIMTVPPPSISGRVSRVAVKAAFFGIMGYSLY
          STELNIQEIMTVPPPS.SGRVS..AVKAAFFG.MGYSL.
Retrocopy STELNIQEIMTVPPPSVSGRVSWLAVKAAFFGVMGYSLH

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_1296 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005772	1 retrocopy	retro_etel_1296 ,