RetrogeneDB ID: retro_etel_1197

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_226497:3066..3686(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010696
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSETEG00000016033
• Aliases: None
• Description: glycolipid transfer protein [Source:HGNC Symbol;Acc:24867]

Sequence

>retro_etel_1197
ATGGCGCTGCTGGCCGAGCACCTCCTGAAGCCGCTGCCCGCCGACAAGCAGATCGAGACCGGGCCCTTCCTGGAGGCCGT
GTCCCACCTGCCGCCCTTCTTCGATTGCCTCGGCTCCCCGGTGTTCACCCCCATCAAGGCCGACATCAGCGGTAACATCA
CGAAAATCAAGGCTGTATATGACACCGATCCCACCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGGAGAAGGAGATG
TATGGAGCCCAGTGGCCCAAGGTGGGGGCCACGCTGGCGCTGATGTGGCTGAAAAGAGGCCTCCGCTTCATCCAGGTCTT
CCTCCAGAGCATCTGCGACGGGGAGCGGGACGAGAACCACCCCAGCCTCATCTGGGTCAACGCCACCAAGGCCTATGAGA
TGGCGCTCAAGAAGTACCACGGCTGGATCGTGCAGAAGATCTTCCAGGCGGCGCTGTGCGCAGCCCCCTATAAGTCTGAC
TTCCTGAAAGCCCTGTCCAAGGGGCAGAATGTGACGGAGGAGGAGTGCCTGGAGAAGACCCGGCTCTTCCTGGTCAACTA
CAGGCCACCATCGACATCATCTACGAGATGTACACCAAGATGAACGCCGAGCTCAACTAC

Alignment

ORF - retro_etel_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTDPTKFRTL
          MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTDPTKFRTL
Retrocopy MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTDPTKFRTL

Parental  QNILEVEKEMYGAQWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPNLIRVNATKAYEMALKKYH
          QNILEVEKEMYGAQWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHP.LI.VNATKAYEMALKKYH
Retrocopy QNILEVEKEMYGAQWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPSLIWVNATKAYEMALKKYH

Parental  GWIVQKIFQAALYAAPYKSDFLKALSKGQNVTEEECLEKTRLFLVNY-TATIDIIYEMYTKMNAELNY
          GWIVQKIFQAAL.AAPYKSDFLKALSKGQNVTEEECLEKTRLFLVNY..ATIDIIYEMYTKMNAELNY
Retrocopy GWIVQKIFQAALCAAPYKSDFLKALSKGQNVTEEECLEKTRLFLVNY<QATIDIIYEMYTKMNAELNY

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_1197 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016033	1 retrocopy	retro_etel_1197 ,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,
Ictidomys tridecemlineatus	ENSSTOG00000004484	1 retrocopy	retro_itri_973,