RetrogeneDB ID: retro_etel_527

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8805:2165..2852(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000016752
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THRA
• Ensembl ID: ENSETEG00000013166
• Aliases: None
• Description: thyroid hormone receptor, alpha [Source:HGNC Symbol;Acc:11796]

Sequence

>retro_etel_527
ATGGAACAGAAGCTAAGCAAGCTGGAGTGTGGGTCGGACCCTGAGGAGAACAGTTCCAGGTTCTCCGATGGAAAGCGAAA
AAGAAAGAATGGCCAATGTCCCCTGAAAACTTGCATGTCAGTGTATATCCCTAGCTACCTGGACAAAGACGAGCAGTGTG
TCATGTGCGGGGACAAGGCAACCGGTTATCACTACCGCTGCATCACTGTGAAGGCTGCAAGGGCTTCTTTCGCCGCACAA
TCCAGAAGAACCTCCCACCCCCACTACTCCTGCAAATATGACAGCTGCTGTGTCATCGACAAGATCACCCGCAACCAGTG
CCAGCTGTGCCGCTTCCGGAAGTGCATCGCTGTGGGCATGGCTATGGACTTGGTTCTAGATGACTCAAAGCGGGTGGCCA
AGCGCAAGCTGATCGAGCAGAACCGGGATAGGCGGCGGAAGGAGATGATCTGCTCACTGCAGCAGCGGCCAGAGCCCACT
CCTGAGGAGTGGGACCTGATCCACGTCGCCACGGAGGCCCATCGCAGCACTAACGCGCAGGGCAGCCACTGGAAGCAGAG
GCGGAAATTCCTGCCGGATGACATTGGCCAGTCCCCCATCGTCTCAATGCCGGACGGAGACAAGGTGGACCTAGAGGCCT
TCAGCGAGTTTACCAAGATCATCACCCCAGCCATCACCCGTGTGGTG

Alignment

ORF - retro_etel_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.4 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEQKPSKLECGSDPEENSARSPDGKRKRKNGQCPLKTSMSGYIPSYLDKDEQCVVCGDKATGYHYRCIT-
          MEQK.SKLECGSDPEENS.R..DGKRKRKNGQCPLKT.MS.YIPSYLDKDEQCV.CGDKATGYHYRCIT.
Retrocopy MEQKLSKLECGSDPEENSSRFSDGKRKRKNGQCPLKTCMSVYIPSYLDKDEQCVMCGDKATGYHYRCIT<

Parental  CEGCKGFFRRTIQKNL-HPTYSCKYDSCCVIDKITRNQCQLCRFRKCIAVGMAMDLVLDDSKRVAKRKLI
          CEGCKGFFRRTIQKNL.HP.YSCKYDSCCVIDKITRNQCQLCRFRKCIAVGMAMDLVLDDSKRVAKRKLI
Retrocopy CEGCKGFFRRTIQKNL>HPHYSCKYDSCCVIDKITRNQCQLCRFRKCIAVGMAMDLVLDDSKRVAKRKLI

Parental  EQNRERRRKEEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVSMPDGD
          EQNR.RRRK.EMI.SLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVSMPDGD
Retrocopy EQNRDRRRK-EMICSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVSMPDGD

Parental  KVDLEAFSEFTKIITPAITRVV
          KVDLEAFSEFTKIITPAITRVV
Retrocopy KVDLEAFSEFTKIITPAITRVV

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_527 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013166	1 retrocopy	retro_etel_527 ,