RetrogeneDB ID: retro_etel_1004

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_199533:2776..3497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMX2
• Ensembl ID: ENSETEG00000001763
• Aliases: None
• Description: RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282]

Sequence

>retro_etel_1004
AACCCTTTGACGAAGGTGAAGCTCATCAATGAGCTGAATGAGCGGAAGGTCCAGCTTGCGGTGGCCGGTGCGGTTTCCTG
GCGCTCTGAGGACAAGGACAGCGCCTGGATCTTCCTGGGAGGCCTTCCTTACGAGCTGACTGAAGGAGACGTCATCTGTG
TGTTCTCACAGTATGGAGAGGTCGTGAACATCAATCTCGTGAGGGACAAGAAGACTGGGAAATCCAAAGGATTCGGTTTC
CTGTGCTATGAAGACCAGAGGAGCACAATCCTGGCTGTGGATAATTTCAATGGGATCAAAATCAAAGGACGGACCATCCG
AGTGGATCACGTGACCAACTATCGGGCTCCGAAGGACTCAGAGGAGTTGGACGAGGTAACCAAAGCCCTGCAGGAGAAGG
GCTGTGGGGCTCACACACCCCCGCCAAGCTCATCGGAGGGCTCAGACAATGACAGACCCACAAAGAAGCACAGAAAAGAC
AAAAAGGGGAAAAAGAAAGGAACGAAAGTCAAAGAGAAGCCTGAGCGGGAGGTCCTGACTGAGCCACTGCCCTCCTCCTC
CTCACCCAGCATCAAGGTGATAACGGAGGAGCCAGGCTTGAAAAAGCACTGCAGCGAGAGCTCCACCAGGGCGCCCACGG
TAGAGGCCAGAGAGGGCCGGAAGCAGCAGCTCAGCTCTCCAGACGGATCGACGGGCAGCAGACCCAGAGAGGAAGGAGAA
G

Alignment

ORF - retro_etel_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.23 %
• Parental protein coverage: 70.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPLTKVKLINELNEREVQLGVAEKVSWHSEYKDSAWIFLGGLPYELTEGDVICVFSQYGEVVNINLVRDK
          .PLTKVKLINELNER.VQL.VA..VSW.SE.KDSAWIFLGGLPYELTEGDVICVFSQYGEVVNINLVRDK
Retrocopy NPLTKVKLINELNERKVQLAVAGAVSWRSEDKDSAWIFLGGLPYELTEGDVICVFSQYGEVVNINLVRDK

Parental  KTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEELDEVTKALQAKGCGAHTP
          KTGKSKGF.FLCYEDQRSTILAVDNFNGIKIKGRTIRVDHV.NYRAPKDSEELDEVTKALQ.KGCGAHTP
Retrocopy KTGKSKGFGFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVTNYRAPKDSEELDEVTKALQEKGCGAHTP

Parental  PPSSSEGSDNERSTKKHKKDKKEKKKRKKAKERPEREVLAEPLPSSSSPSIKVIPEEPGLKKHYSKSSNR
          PPSSSEGSDN.R.TKKH................PEREVL.EPLPSSSSPSIKVI.EEPGLKKH.S.SS.R
Retrocopy PPSSSEGSDNDRPTKKHXXXXXXXXXXXXXXXXPEREVLTEPLPSSSSPSIKVITEEPGLKKHCSESSTR

Parental  APTAEAREGRKQQPSS-QTD-DAADPERKEK
          APT.EAREGRKQQ.SS.QTD..AADPERKEK
Retrocopy APTVEAREGRKQQLSS>QTDRRAADPERKEK

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_1004 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002436	2 retrocopies	retro_cjac_3040, retro_cjac_4128,
Equus caballus	ENSECAG00000008257	1 retrocopy	retro_ecab_664,
Echinops telfairi	ENSETEG00000001763	1 retrocopy	retro_etel_1004 ,
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2,