RetrogeneDB ID: retro_etel_692

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_145388:302..782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSETEG00000007250
• Aliases: None
• Description: transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]

Sequence

>retro_etel_692
AGATCCGGGAGGCATTCTCATAGACGCTACACTCGATCCAGATCCCACTCTGCTTCGCGAAGTAGCTCACACACACCGGA
CTACCTCCCGACGCCCAAGGGGGCCAAGTCGAACTCGCTCTCCAATGTGCAACCCGAGAAGACACACAGGCTGCAGTGCA
AATCCGAATTGCAACACTCCCCTCGGCGTTTCTGGCCTCAGTTTGTACACAATAGAGAGAGATCTTCATGAAGTATTCTC
TTGATATGGACCATTGAGTGGTGTGATTGTGGTTTATGATCAGTGAACTGGACGGTCTCAAGGGTTGCTTTTGCTTATTT
TGAAAGAATAGATGTCTCAAAGGAGGCTATGCAAAGGGCAAATGGAATGGCGCTAGACGCTAGAAGAATTCGTTTGGATC
GCTCTCTCATCAAGAGGGCACACACACCTGCACCAGGCACCGACATGGGCACACCACCTCACAGTGGTCGAGGAGGGGGG

Alignment

ORF - retro_etel_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSRRHSHRRYTRSRSHSHSHRR-RSRSRSYTPDYRRRRSRSRSHSPMSNRRRHTGSRANPDPNTCLGVFG
          RS.RHSHRRYTR....S.SH...R..........RR.R..SR..SPM.N.RRHTG..ANP..NT.LGV.G
Retrocopy RSGRHSHRRYTR----SRSHSA>REVAHTHRTTSRRPRGPSRTRSPMCNPRRHTGCSANPNCNTPLGVSG

Parental  LSLYTTERDLREVFSRYGPLSGVNVVYDQRTGRSRGF-AFVYFERIDDSKEAMERANGMELDGRRIRVDY
          LSLYT.ERDL.EVFS.YGPLSGV.VVYDQ.TGRS.G..AF.YFERID.SKEAM.RANGM.LD.RRIR.D.
Retrocopy LSLYTIERDLHEVFS*YGPLSGVIVVYDQ*TGRSQGL<AFAYFERIDVSKEAMQRANGMALDARRIRLDR

Parental  SITKRAHTPTPGIYMGRPTHSGGGGG
          S..KRAHTP.PG..MG.P.HSG.GGG
Retrocopy SLIKRAHTPAPGTDMGTPPHSGRGGG

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_692 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692 ,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,