RetrogeneDB ID: retro_etel_2047

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_40846:1560..2316(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HIAT1
• Ensembl ID: ENSETEG00000005809
• Aliases: None
• Description: hippocampus abundant transcript 1 [Source:HGNC Symbol;Acc:23363]

Sequence

>retro_etel_2047
TTAAAAAAAGTGGGCCAAGACAACATAGTGCTGCTAATCTGCATCAAGGTATTTCTCTCCTACCTACCAGAGGCAGGCCA
ATATTCCAGCTTGTTTTTATACCTCAGACAGATAATGAAATTTTCACCAGAAAGTGTTGCAGCATTTATAGCAGTTCTTG
GCATTCTTTCCATTATTGCACAGACTGTAGTCTTGAGTTTACCTATGAGGTCGATTGGAAATAAAAGCACCATTTTATTG
GGTCTGGGATTTCAAATACTACAGCTGGCATGGTATGGCTTTGGTTCAGAGCCTTGGATGATGTGGGCTGCTGGGGCAGT
GGCAGCCATGTCTAGCATTACCTTCCCAGCTGTCAGTGCACTTGTTTCACGAACTGCTGATGCCGATCAACAAGGTGTTG
TTCAAGGAATGATAACAGGAATTCGAGGGTTGTGCAATGGTCTGGGACCTGCCCTTTATGGATTCATCTTCTACATATTC
CACGTGGAACTTAAAGAACTGCCAATAACAGGAACCGACTTGGGAACAAACACAAGCCCCAGCAGCACTTTGAACATCAT
CATCCCTGGGCCCCCATTCCTCTTTGGAGCCTGTTTGGTACTGCTGGCTCTGCTCATTGCCTTGTTTATTCCGGAACATA
TCAACTTGAGCTTAAGGTCCAGCAGTTGGAAAAAGCACTGTGGTGCTCACAGCCATCCTCACAGTACACAAGCCCCCGGA
GAGGCCAAAGAACCTTTACTCCAAGACACAAATGTG

Alignment

ORF - retro_etel_2047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.19 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKKVGQDSIVLLICITVFLSYLPEAGQYSSFFLYLRQIMKFSPESVAAFIAVLGILSIIAQTIVLSLLMR
          LKKVGQD.IVLLICI.VFLSYLPEAGQYSS.FLYLRQIMKFSPESVAAFIAVLGILSIIAQT.VLSL.MR
Retrocopy LKKVGQDNIVLLICIKVFLSYLPEAGQYSSLFLYLRQIMKFSPESVAAFIAVLGILSIIAQTVVLSLPMR

Parental  SIGNKNTILLGLGFQILQLAWYGFGSEPWMMWAAGAVAAMSSITFPAVSALVSRTADADQQGVVQGMITG
          SIGNK.TILLGLGFQILQLAWYGFGSEPWMMWAAGAVAAMSSITFPAVSALVSRTADADQQGVVQGMITG
Retrocopy SIGNKSTILLGLGFQILQLAWYGFGSEPWMMWAAGAVAAMSSITFPAVSALVSRTADADQQGVVQGMITG

Parental  IRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTNTSP-QHHFEQNSIIPGPP-FLFGACSVLLALLV
          IRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTNTSP.Q.HFE.....P..P.FLFGAC.VLLALL.
Retrocopy IRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTNTSP<QQHFEHHH--PWAP>FLFGACLVLLALLI

Parental  ALFIPEHTNLSLRSSSWKKHCGGHSHPHSTQAPGEAKEPLLQDTNV
          ALFIPEH.NLSLRSSSWKKHCG.HSHPHSTQAPGEAKEPLLQDTNV
Retrocopy ALFIPEHINLSLRSSSWKKHCGAHSHPHSTQAPGEAKEPLLQDTNV

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_2047 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010468	1 retrocopy	retro_chof_2174,
Echinops telfairi	ENSETEG00000005809	1 retrocopy	retro_etel_2047 ,
Myotis lucifugus	ENSMLUG00000002112	1 retrocopy	retro_mluc_718,
Oryctolagus cuniculus	ENSOCUG00000007819	1 retrocopy	retro_ocun_1386,
Drosophila melanogaster	FBgn0035400	1 retrocopy	retro_dmel_13,