RetrogeneDB ID: retro_etel_1959

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_319784:87975..88596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA2
• Ensembl ID: ENSETEG00000014816
• Aliases: None
• Description: pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]

Sequence

>retro_etel_1959
GAGACTGTGCTTAATATGGTTGTAGAAGTACCGCGATGGACAAATGCTAAAATGGAGATTGCCACCAAGGATCCCCTGAA
TCCCATTAAACAGGATGTGAAGCGGGTTATGCTGTGCTATGAGGCGAATATCTTCCCTCACAAGGGTTACATATGGAATT
ACAGTGCCCTCCCTCAGACTTGGGAAGAGCCTCATTATAAAGATAAGAGTACAGATTGCTGTGGAGATGATGACCCCATT
GATGTTTGTGAAATAGGCTCAAAGATTTTTTCTCGTGGAGAGATCATCCAAGTCAAGATCCTTGGGATTTTGGCTCTTAT
TGATGAAGGTGAAACTGATTGGAAAGTAATTGCTGTCTATATGAATGATCTGGAAGCCTCAAAGATTCATGATATCGATG
ATGTTAAGAAGTACAAACCAGGTTACTTGGAGGCTATGCTTAATCGGTTTAGATTGTATAAAGTACCAGAAGGAAAACCA
GAAAACAAGTTTGCTTTTAATGGGGAATTTAAAAACAAGGCTTTTGCCCTTTAAGTTATTAAATCTGCTCATGAATGTTG
GAAAGCATTGCTTATGAAGAAATGTGACAGAGAGGCTATAAATTGCACTAACAGGTATGTG

Alignment

ORF - retro_etel_1959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 59.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETLFNMVVEVPRWTNAKMEIATKEPLNPIKQDVKGGMLRYVANIFPHKGYIWNYGALPQTWEDPHHKDKN
          ET..NMVVEVPRWTNAKMEIATK.PLNPIKQDVK..ML.Y.ANIFPHKGYIWNY.ALPQTWE.PH.KDK.
Retrocopy ETVLNMVVEVPRWTNAKMEIATKDPLNPIKQDVKRVMLCYEANIFPHKGYIWNYSALPQTWEEPHYKDKS

Parental  TDCCGDNDPIDVCEIGSKIFSRGEVIQVKILGILALIDEGETDWKVIAINVNDPEASKIHDINDVKKYKP
          TDCCGD.DPIDVCEIGSKIFSRGE.IQVKILGILALIDEGETDWKVIA...ND.EASKIHDI.DVKKYKP
Retrocopy TDCCGDDDPIDVCEIGSKIFSRGEIIQVKILGILALIDEGETDWKVIAVYMNDLEASKIHDIDDVKKYKP

Parental  GYLEATLNWFRLYKVPEGKPENKFAFNGEFKNKAFALEIIKSTHECWKALLMKKCDRGAINCTNAQV
          GYLEA.LN.FRLYKVPEGKPENKFAFNGEFKNKAFAL..IKS.HECWKALLMKKCDR.AINCTN..V
Retrocopy GYLEAMLNRFRLYKVPEGKPENKFAFNGEFKNKAFAL*VIKSAHECWKALLMKKCDREAINCTNRYV

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_1959 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959 ,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,