RetrogeneDB ID: retro_etel_2019

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_325378:1225..1648(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: USF1
• Ensembl ID: ENSETEG00000015715
• Aliases: None
• Description: upstream transcription factor 1 [Source:HGNC Symbol;Acc:12593]

Sequence

>retro_etel_2019
CAAGTGATGCACAGGGTGATCCAGGTGTCTGAAGGGAAGCTGGATGGCCAGGCTGAAGACACTGGAGCCATCAGTGGTTA
CCCTGACACGCAATGCATGACCCAGGCGGTGATCTACGGTACGTTCACCAATGACAATGCAGTTGATGCAGAAGGCACAG
CTGCAGAGACATGTTATAGGCACTTGCCCAGCACTGCAGTGAGAGATGGGGTAGGGGAAACCACATGGGGAAACACAACT
GCTGTTGATACTACCTGGGGCTCAGAGGCACTACAGGGACAGCAACTCCTCCTGGCACTGGGCAGTTCTTTATCAATGAT
GTCACTACAAGAGGTGTTGCAAGGAAAATCCAGTACTCCATTGCCCCTCAGGACCCACCCTTATTCCCTGAAATCAGAAG
CTCCCCGATACTCGAGATGAGAA

Alignment

ORF - retro_etel_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 62.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVMYRVIQVSEGQLDGQTEGTGAISGYPATQSMTQAVIQGAFTSDDAVDAEGTAAETHYTYFPSTAVGDG
          QVM.RVIQVSEG.LDGQ.E.TGAISGYP.TQ.MTQAVI.G.FT.D.AVDAEGTAAET.Y...PSTAV.DG
Retrocopy QVMHRVIQVSEGKLDGQAEDTGAISGYPDTQCMTQAVIYGTFTNDNAVDAEGTAAETCYRHLPSTAVRDG

Parental  AGGTTSGSTAAVVTTQGSEALLGQ-ATPPGTGQFFV-MMSPQEVLQGGSQRSIAPRTHPYSPKSEAPRTT
          .G.TT.G.T.AV.TT.GSEAL.GQ.ATPPGTGQFF..MMS.QEVLQG.S......RTHPYS.KSEAPR..
Retrocopy VGETTWGNTTAVDTTWGSEALQGQ<ATPPGTGQFFI>MMSLQEVLQGKSSTPLPLRTHPYSLKSEAPRYS

Parental  RDE
          R.E
Retrocopy R*E

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_2019 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015715	1 retrocopy	retro_etel_2019 ,
Mus musculus	ENSMUSG00000026641	1 retrocopy	retro_mmus_727,