RetrogeneDB ID: retro_etel_401

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_6787:77520..78108(-)
• Located in intron of: ENSETEG00000002781

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIM2
• Ensembl ID: ENSETEG00000007968
• Aliases: None
• Description: pim-2 oncogene [Source:HGNC Symbol;Acc:8987]

Sequence

>retro_etel_401
ATGTTGACCAAACCTCAGCCTGAGCTTCCCGCGCCCCCCGTACCCCCCACGCTGCCGCCAGGAGGCAAGAATCAAGAAGC
ATTTGAAGCCGAATGCCGACTTGGCACTGTACTGGGCAAAGGGGGCTTTGGTACGGTCTTCGCGGCACACCGGGTAGCGG
ACCGACTCCAGGTGGCCATCAAAGTGATACCGCGGAATCGGGTGCTGGGCAGTTTCCCTCTGACCAACTCGGCCACATGC
CCACTCGAGGTGGCCCTGCGATGGAAGGTGGGTGCCGGTGGTGGACACCCAGGTGTGATATGCCTGCTCGACTGGTTTGA
GACACTAGAGGGCGTCATGCTGGTTCTCGAGCGACCTTCACCTGCCCAGGATCTCTCTGACGATATCACGGAGCTGGGTC
CACTGGGTGAGAGCCGAAGCCGCTGCCTCTTTGCCCAGGTAGTGTCAGCTGTCAGGCACTGCCATGCCTGCGGAGTTGTC
CACCGTGATATCAAGGACGAGACCATACCGATAGATCTCCGCCGACGCTGTGCCAAACTCATTGATTATGGGTCTGGCGC
CCTGCTGCATGATGAGCCCTACACTGAC

Alignment

ORF - retro_etel_401 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 63.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLTKPQPELPAPPVAPTLPPGGKNQEAFEAEYRLGTVLGKGGFGTVFAGHRVADRLQVAIKVIPRNRVLG
          MLTKPQPELPAPPV.PTLPPGGKNQEAFEAE.RLGTVLGKGGFGTVFA.HRVADRLQVAIKVIPRNRVLG
Retrocopy MLTKPQPELPAPPVPPTLPPGGKNQEAFEAECRLGTVLGKGGFGTVFAAHRVADRLQVAIKVIPRNRVLG

Parental  SFPLDNSATCPLEVALLWKVGASGGHPGVIRLLDWFETLEGVMLVLERPSPAQDLFDYITEQGPLGESRS
          SFPL.NSATCPLEVAL.WKVGA.GGHPGVI.LLDWFETLEGVMLVLERPSPAQDL.D.ITE.GPLGESRS
Retrocopy SFPLTNSATCPLEVALRWKVGAGGGHPGVICLLDWFETLEGVMLVLERPSPAQDLSDDITELGPLGESRS

Parental  RCLFAQIVSAVRHCHACGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTD
          RCLFAQ.VSAVRHCHACGVVHRDIKDE.I.IDLRR.CAKLID.GSGALLHDEPYTD
Retrocopy RCLFAQVVSAVRHCHACGVVHRDIKDETIPIDLRRRCAKLIDYGSGALLHDEPYTD

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_401 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401 ,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223, retro_sara_395,