RetrogeneDB ID: retro_etel_2097

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_55253:1094..1656(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM248
• Ensembl ID: ENSETEG00000015971
• Aliases: None
• Description: transmembrane protein 248 [Source:HGNC Symbol;Acc:25476]

Sequence

>retro_etel_2097
AGGCCTTTCGGGGGGGTACTTGCACAACGTCACCCACCTGCACTCGACCGTCCTAGGACAGCAGATTGGGCTCCCAGGCA
GGGAGGCCCACGAGGAGATCATTGTCACCTTCACGCTGCCCACAGCCTGGAGCGCTGATGACTGCGCACTCCACGGCCCT
GCGAGCAGGTGGTCTTCACGGCCTGCGTGACCCTCACTGCCGCCCTTGGTGTGCTCCCTGTCACCGTATAGCCTCCACCT
GCATCCCGGACACACACAGCACCGCCATGCTCTGGTAGAAGATCTTCACCACAGCCAGAGACACCAACATGAAGTACAAC
CAAGACTACCATCCCTTCTGGTGTTGCAAGGGTGCTATTGGGCGTCTGCCGTGCTTTCAGCCCCAAGCTCACAGTCATTG
TTCCCGATGACGACCGCTCCCTGGTAAACCTGCACCTCATGCACGCCAGCGGCTCCCTCTCCCCGATGGTGATAACCATG
TGCTGCTATACACGTTGTCAAAGGCAGACCGAGCAAACTATGTCAGAGCAATCCTGGATTCCGTCCCGAGCAGGTGGCTT
TG

Alignment

ORF - retro_etel_2097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.2 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RPFGG-YSRNVTHLYSTVLGQQIGLSGREAHEEINVTFTLPTAWSADDCALHG-HCEQVVFTTCMTLTAA
          RPFGG.Y..NVTHL.STVLGQQIGL.GREAHEEI.VTFTLPTAWSADDCALHG..CEQVVFT.C.TLTAA
Retrocopy RPFGG>YLHNVTHLHSTVLGQQIGLPGREAHEEIIVTFTLPTAWSADDCALHG<PCEQVVFTACVTLTAA

Parental  LGVFPVTVQPP-HCIPDTYSNATLWYKIFTTARDANTKYAQDYNPFWCYKGAIGKVYHAFNP-KLTVIVP
          LGV.PVTV.PP..CIPDT.S.A.LW.KIFTTARD.N.KY.QDY.PFWC.KGAIG.....F.P.KLTVIVP
Retrocopy LGVLPVTV*PP<TCIPDTHSTAMLW*KIFTTARDTNMKYNQDYHPFWCCKGAIGRL-PCFQP>KLTVIVP

Parental  DDDRSLINLHLMHTSYFLFVMVITMFCYA-VIKGRPSKLRQSNPEFCPEKVAL
          DDDRSL.NLHLMH.S..L..MVITM.CY..V.KGRPSKL.QSNP.F.PE.VAL
Retrocopy DDDRSLVNLHLMHASGSLSPMVITMCCYT>VVKGRPSKLCQSNPGFRPEQVAL

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_2097 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097 ,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,