RetrogeneDB ID: retro_etel_1749

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_291713:3127..3349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SS18L2
• Ensembl ID: ENSETEG00000007192
• Aliases: None
• Description: synovial sarcoma translocation gene on chromosome 18-like 2 [Source:HGNC Symbol;Acc:15593]

Sequence

>retro_etel_1749
ATGTCTGTGGCCTTTGTACTGGACTGGCTGCAGGCAAAGAGGAAGTGAATCAGAGACTGTTCTGGAAAGAGAATGACCAG
CTGATTGGCTGTAAGGTAGATGATCAGAACAAAGGCCGGGTCAACGAAAGTGTCCAGTACCACTTTGGTGCTACACCAAA
ATCGGATTTATTTGGCTACCATTGCCGAAGTCAGCCCAACCAGCACTCCAAAACCACTGGAG

Alignment

ORF - retro_etel_1749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVAFVPNWLR-GKAEVNQETIQRLLEENDQLIRCIVEYQNKGRANECVQYQH-VLHRNLIYLATIADAS
          MSVAFV..WL..GK.EVNQ........ENDQLI.C.V..QNKGR.NE.VQY...VLH.N.IYLATIA..S
Retrocopy MSVAFVLDWLQ<GKEEVNQRLFWK---ENDQLIGCKVDDQNKGRVNESVQYHF>VLHQNRIYLATIAEVS

Parental  PSSTPKPLE
          P.STPKPLE
Retrocopy PTSTPKPLE

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_1749 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Erinaceus europaeus	ENSEEUG00000014065	1 retrocopy	retro_eeur_634,
Echinops telfairi	ENSETEG00000007192	2 retrocopies	retro_etel_1749 , retro_etel_2074,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Mus musculus	ENSMUSG00000032526	3 retrocopies	retro_mmus_1247, retro_mmus_1827, retro_mmus_3284,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Sorex araneus	ENSSARG00000014056	1 retrocopy	retro_sara_465,
Tarsius syrichta	ENSTSYG00000007658	1 retrocopy	retro_tsyr_1687,