RetrogeneDB ID: retro_etel_1585

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_280686:48801..49383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX4
• Ensembl ID: ENSETEG00000002650
• Aliases: None
• Description: pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:13403]

Sequence

>retro_etel_1585
ACCCACGTGATGAATCTCCTGCGAGAGCAGAGCCGGACCAGGCCCATCTCCCCGAAGGAGATCGAGCGGATGGTCAGTAT
CATCCACCGCAAGTTCAGCTCCATCCAGATGCAGCTCAAGCAGAGCACGTGTGAGGCGGTCATGATCCTGCGTTCCCGGT
TCCTGGATGCGCGGCGGAAGAGACGGAATTTCAACAAGCAAGCTACGGAAATCCTGAATGAATATTTCTATTCCCATCTC
AGCAACCCTTACCCCAGTGAGGAAGCCAAAGAGGAGTTAGCCAAGAAGTGTGGCATCACAGTCTCCCAGGTATCAAACTG
GTTTGGAAATAAGCGAATCCGGTACAAGAAGAACATAGGTAAATTCCAAGAGGAAGCCAATATTTATGCTGCCAAAACGG
CTGTCACTGCTACCAATGTGTCAGCCCATGGAAGCCAAGCTAACTCACCCTCAACTCCCAACTCAGCTGGTTCTTCCAGT
TCTTTTAACATGTCAAACTCTGGAGATTTGTTCATGAGCGTGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGT
TGGAGCCAACGTGCAATCACAG

Alignment

ORF - retro_etel_1585 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.68 %
• Parental protein coverage: 63.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THVTNLLREQSRVRPVSPKEMEHMVGVIHGKFRAIQMQLKQSTCEAVMTLRSRFLDARRKRRNFSKQATE
          THV.NLLREQSR.RP.SPKE.E.MV..IH.KF..IQMQLKQSTCEAVM.LRSRFLDARRKRRNF.KQATE
Retrocopy THVMNLLREQSRTRPISPKEIERMVSIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATE

Parental  VLNEYFYSHLSNPYPSEEAKEELARKGGITVSQVSNWFGNKRIRYKKNMGKFQEEANVYVSKTSVDATKV
          .LNEYFYSHLSNPYPSEEAKEELA.K.GITVSQVSNWFGNKRIRYKKN.GKFQEEAN.Y..KT.V.AT.V
Retrocopy ILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNV

Parental  GSPGHQASCPLTP-SSGSSSTFSLTCPEDASVSLQALASD--QPFQMGPRSQSQ
          ...G.QA..P.TP.S.GSSS.F......D...S.Q.L..D..Q..Q.G...QSQ
Retrocopy SAHGSQANSPSTPNSAGSSSSFNMSNSGDLFMSVQSLNGDSYQGAQVGANVQSQ

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_1585 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002650	1 retrocopy	retro_etel_1585 ,