RetrogeneDB ID: retro_etel_530

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8833:471..1324(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000012165
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GDAP2
• Ensembl ID: ENSETEG00000004391
• Aliases: None
• Description: ganglioside induced differentiation associated protein 2 [Source:HGNC Symbol;Acc:18010]

Sequence

>retro_etel_530
GCTACCTACCAAAGGCTGCTACCTCTGTATTTCCCAAGGTCGTTGGAGGAGGAGAGCCAGTCATTGCCATACCTTCCTGC
GGATATTGGAAATTCAGAAGTGGAGCCTGTAGTACCTGAACGGCAGATTAGGATAAGTGAAAAGCCTGGTGCCCCCGAGG
ATGACCAGGAAGAAGAGGAGGGTTTGGGAGTTGACCTCTCTTTCATTGGCTCTCATGCATTTGCTCAAATGGGAAGGAGA
TATTGATAAGCAAAGAAGATTGATCCTCCAGGGACAGTTATCAGAGGCAGCCCTACAGAAGCAGCATCAAAGAAATTATA
ATTGTTGGTTATGCCAAGCAAGATCTGAGGATCTGTCCCATATTGCTTCTCTAAAAGCTTTATACCAAACAGGTGTTGAT
AACTGTGGCTGCACCGTGATGGTGGTAGTTGGAAGAAACATCCCTGTAACATTAATAGATATGGACAAGGCTCTCCTGTA
TTTCATCCATGTAACGGATCACATCGCTGTGAAGGAATATGTATTAGTGTATTTTCACACACTGACCAGCGAATACAATC
ACCTCGACTCCGATTTCCTGAAGAAACTCTATGATGTTGTGGATGTCAAGTACAAAAGGAATTTAAAGGCTGTATATTTT
GTTCATCCAACATTTCGTTCAAAGGTGTCAACATGGTTTTTTACTACCTTTTCTGTCTCAGGACTGAAGGACAAAATCCA
CCATGTGGATAGCCTCCACCAGCTATTTTCTGCCATATCTCCAGAACAGATCGACTTTCCTCCTTTTGTCCTTGAATATG
ATGCTCGGGAAAATGGGCCATAGTATACATCGGATCCCCCGTCACCAGATTTC

Alignment

ORF - retro_etel_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.82 %
• Parental protein coverage: 57.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATYQRLLPLYFPRSLEEESQSLPYLPADIGNSEGEPVVPERQIRISEKPGAPEDDQEEEEGLGVDLSFIG
          ATYQRLLPLYFPRSLEEESQSLPYLPADIGNSE.EPVVPERQIRISEKPGAPEDDQEEEEGLGVDLSFIG
Retrocopy ATYQRLLPLYFPRSLEEESQSLPYLPADIGNSEVEPVVPERQIRISEKPGAPEDDQEEEEGLGVDLSFIG

Parental  SHAFARM-EGDIDKQRRLILQGQLSEAALQKQHQRNYNRWLCQARSEDLSDIASLKALYQTGVDNCGXXX
          SHAFA.M.EGDIDKQRRLILQGQLSEAALQKQHQRNYN.WLCQARSEDLS.IASLKALYQTGVDNCG...
Retrocopy SHAFAQM>EGDIDKQRRLILQGQLSEAALQKQHQRNYNCWLCQARSEDLSHIASLKALYQTGVDNCGCTV

Parental  XXXXXXXXXXXXXXXXXALLYFIHVMDHIAVKEYVLVYFHTLTSEYNHLDSDFLKKLYDVVDVKYKRNLK
          .................ALLYFIHV.DHIAVKEYVLVYFHTLTSEYNHLDSDFLKKLYDVVDVKYKRNLK
Retrocopy MVVVGRNIPVTLIDMDKALLYFIHVTDHIAVKEYVLVYFHTLTSEYNHLDSDFLKKLYDVVDVKYKRNLK

Parental  AVYFVHPTFRSKVSTWFFTTFSVSGLKDKVHHVDSLHQLFSAISPEQVDFPPFVLEYDARENGPYYTSDP
          AVYFVHPTFRSKVSTWFFTTFSVSGLKDK.HHVDSLHQLFSAISPEQ.DFPPFVLEYDARENGP.YTSDP
Retrocopy AVYFVHPTFRSKVSTWFFTTFSVSGLKDKIHHVDSLHQLFSAISPEQIDFPPFVLEYDARENGP*YTSDP

Parental  PSPDF
          PSPDF
Retrocopy PSPDF

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_530 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012907	2 retrocopies	retro_chof_1607, retro_chof_2559,
Echinops telfairi	ENSETEG00000004391	1 retrocopy	retro_etel_530 ,
Felis catus	ENSFCAG00000003468	1 retrocopy	retro_fcat_1125,
Mus musculus	ENSMUSG00000027865	1 retrocopy	retro_mmus_2225,