RetrogeneDB ID: retro_etel_490

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8189:91944..92717(+)
• Located in intron of: ENSETEG00000007170

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS2
• Ensembl ID: ENSETEG00000015746
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7708]

Sequence

>retro_etel_490
GAAAAGAGAGAAGATGTTTGAGTTCTATGAGTGAGTGTCCCGTCGCCCTGAGTGCACGCTGCTTACGTCAGGCCAGGAGG
CGTGTACCAGTACCTACCCTCGAGCTCATAGATGACATCTATGAGTTTTCTGAGAACTTCCTATCCGGATTGATGAGGTG
GAGGAGATGCTGACCAACAACAGGATCTGGCGATATCGCACAGTGGACATCAGGGTTGTAACAGCAGAGGATGCCCTTAA
CTATGGTTTCAGTGGGGTGATGCTCCGGGGCTCCGGTATCCAGTGAGTCCTTCAGAAGGCATAGCCCTATGATGTGTATG
ACCAGGTGGAGTTTGATGTTCCCATTGGCTCCCAAGGGGACTGCTACGATCGGTACCTGTGTTGGGTGGAGGAGATGCGC
CAGTCCCTTTGGATCATCCTACAGTTTTTTAACAAGATACCTCCTGGGGAGATCAAGGTGGATGACGCCAAAAGTGTCTC
CTCTAAAGCGATCCGAGGGGAAGACTTCCATGGAGTCGCTGATTCACCATTTTAAGCTGCACACCGAGGGCTACCAGGTT
CCTCCAGGGGCCACTTACACTGCCATTGAGGCTCCTAAGGGCGAGTTTGGTGTATACCTGGTGTCTGATGGCAGCAGCCG
CTCGTATTGATGCAAGATCAAGGCGCCTGGTTTTGCCCACTTGGCTGGTTTGGAAAAGATGTCCAAGGGACACATGCTGG
TAGATGGTGTCATCATAGGTACCCAAGACATTGTGTTTGGAGAAGTAGATCGG

Alignment

ORF - retro_etel_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.06 %
• Parental protein coverage: 55.84 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEREKMFEFYERVSGARMHAAYVRPGGVHQDLP-LGLMDDIYEFSKNF-SLRIDEVEEMLTNNRIWRNRT
          E.RE........V.....HAAYVRPGGV.Q.LP.L.L.DDIYEFS.NF...RIDEVEEMLTNNRIWR.RT
Retrocopy EKREDV*VL*VSVPSP*VHAAYVRPGGVYQYLP<LELIDDIYEFSENF<PIRIDEVEEMLTNNRIWRYRT

Parental  VDIGVVTAEDALNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFDVPIGSHGDCYDRYLCRVEEMRQSLR
          VDI.VVTAEDALNYGFSGVMLRGSGIQ..L.K..PYDVYDQVEFDVPIGS.GDCYDRYLC.VEEMRQSL.
Retrocopy VDIRVVTAEDALNYGFSGVMLRGSGIQ*VLQKA*PYDVYDQVEFDVPIGSQGDCYDRYLCWVEEMRQSLW

Parental  IILQCLNKMPPGEIKVDDA-KVSP-KRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYL
          IILQ..NK.PPGEIKVDDA.KVSP.KR.E.KTSMESLIHHFKL.TEGYQVPPGATYTAIEAPKGEFGVYL
Retrocopy IILQFFNKIPPGEIKVDDA>KVSPLKRSEGKTSMESLIHHFKLHTEGYQVPPGATYTAIEAPKGEFGVYL

Parental  VSDGSSRPYRCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEVDR
          VSDGSSR.Y.CKIKAPGFAHLAGL.KMSKGHML.D.V.IIGTQDIVFGEVDR
Retrocopy VSDGSSRSY*CKIKAPGFAHLAGLEKMSKGHMLVDGV-IIGTQDIVFGEVDR

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_490 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015746	1 retrocopy	retro_etel_490 ,
Rattus norvegicus	ENSRNOG00000038372	1 retrocopy	retro_rnor_2250,