RetrogeneDB ID: retro_etel_1972

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_320987:11830..12503(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBC1D20
• Ensembl ID: ENSETEG00000011697
• Aliases: None
• Description: TBC1 domain family, member 20 [Source:HGNC Symbol;Acc:16133]

Sequence

>retro_etel_1972
ATGCCGGATGAACAGACAGAGGGGCTCCATGAAGAGTTGATTGATGTCATCCTCCTCCTCGTCTTGCAGCAGAACCCTCA
TCTGCACTACTACCAGGGCTACCATGACATCGTGGTCACGTTTCTGCTGGTGGTAGGCGAGAGGCTGGCCACACCCCTGG
TAGAGAAACTGTCTACCCACCACCTCAGGGATTTCATGGAATCAACCATGGACAACACCAAGCACATCCTAAACTATTTG
ATGACCATCATTGACCAGGTGAACCCAGAACTCCATGACTTCATGCAAAGTGCCGACGTGGGGCCCATCTTTGCCCTCAG
CTGGCTCATCACCTGGTTTGGACACGTCCTGTCCGACTTCAGGCACGTTGTGCGGTTATACGACTTCTTCCTGGCCTGCC
ACCCTCTGATGCCCATTTACTTTGCAGCGGTGATCGTGCTGCACCGAGAGCAGGAGGTCCTGGACAGCGACTGTGACATG
GCCTTCCGTCCACCATCTGCTTTCCCAGGTCCCCCAGGACCTGTCCTACGAGACACTCATCAGCCGGGCCAGAGACCTCT
TTGTCCAGTTCCCCCCGTCCCGGCTCGCTCGGGAGGTGGCCACCCCGCAGCAGGCCAAGAGAACTGCAGCCTCGACCTTC
AAGGACTTTGAACGACATGATGCTGCGGCGCGG

Alignment

ORF - retro_etel_1972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 55.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPDEQREGLQEELIDVILL-ILQQNPQLHYYQGYHDIVVTFLLVVGERLATPLVEKLSTHHLRDFMEPTM
          MPDEQ.EGL.EELIDVILL..LQQNP.LHYYQGYHDIVVTFLLVVGERLATPLVEKLSTHHLRDFME.TM
Retrocopy MPDEQTEGLHEELIDVILLLVLQQNPHLHYYQGYHDIVVTFLLVVGERLATPLVEKLSTHHLRDFMESTM

Parental  DNTKHILNYLMPIIDQVNPELHDFMQSAEVGTIFALSWLITWFGHVLSDFRHVVRLYDFFLACHPLMPIY
          DNTKHILNYLM.IIDQVNPELHDFMQSA.VG.IFALSWLITWFGHVLSDFRHVVRLYDFFLACHPLMPIY
Retrocopy DNTKHILNYLMTIIDQVNPELHDFMQSADVGPIFALSWLITWFGHVLSDFRHVVRLYDFFLACHPLMPIY

Parental  FAAVIVLHREQEVLDCDCDMA-SVHHLLSQIPQDLPYETLISRAGDLFVQFPPSRLAREVAAQQQAERTA
          FAAVIVLHREQEVLD.DCDMA.SVHHLLSQ.PQDL.YETLISRA.DLFVQFPPSRLAREVA..QQA.RTA
Retrocopy FAAVIVLHREQEVLDSDCDMA>SVHHLLSQVPQDLSYETLISRARDLFVQFPPSRLAREVATPQQAKRTA

Parental  ASTFKDFELVSAQQR
          ASTFKDFE...A..R
Retrocopy ASTFKDFERHDAAAR

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_1972 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	ENSETEG00000011697	1 retrocopy	retro_etel_1972 ,