RetrogeneDB ID: retro_etel_844

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_174722:2744..3244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGH
• Ensembl ID: ENSETEG00000008623
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class H [Source:HGNC Symbol;Acc:8964]

Sequence

>retro_etel_844
GGTGGAGGGCGTCAGTGGCAGTGGGGCCATCTGGCCCTACAGTGCTGCTACTCCTCTCCTCCATGCCAGGAGTTCTGCCT
CAACTGCCCTCAGCTCTCACTACGCTTGCTCACCAGGGTCACCTGCACCCTTGAGAACAGCATGGGCCTCTCTTCTGCCA
TCTTCCAAACCCTCTTAGGCTTGCTTGGTTACCTTCATCTTGTGAAGATTGATCAGGAGACTCTATTAATCATTGATTCC
CTGGGCACCCTGATGACTTCTTCCTATGCCTCAGGAACCGCCTTCATCGAGATGGGCTAGGTGAAGGATATTTTCATTAA
CGAGGCTATTTACATAGGGAAGGTCACTTACTATCTCTGCATTTTATTGAAGGACCCACTGGAACCACATGGCATATCCC
AAGTAGTAACTGTCTTCCAGAGTGCCAAACCCTGGCTGGCCGGCTTGAGCAGAGTGTGTAGCAGATCCTGGCACACCAGA
AAGTCACATCCACAAGTCCA

Alignment

ORF - retro_etel_844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.67 %
• Parental protein coverage: 94.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGRLALQRRHYSPSCREFCLSCPRLSLRSLTAVTCSVWLAAYALFTLFENSVILSAAIFITLLGLLGYLH
          GG....Q..H....C...C.S.P......L.....S..L......TL.ENS..LS.AIF.TLLGLLGYLH
Retrocopy GGGRQWQWGHLALQC---CYSSPPCQEFCLNCPQLSLRLLTRVTCTL-ENSMGLSSAIFQTLLGLLGYLH

Parental  FVKIDQETLLIIDSLGIQLTSSYASGKESTTFIEMGKVKDIIINEAIYMQKVIYYLCILLKDPLEPHGIS
          .VKIDQETLLIIDSLG...TSSYASG...T.FIEMG.VKDI.INEAIY..KV.YYLCILLKDPLEPHGIS
Retrocopy LVKIDQETLLIIDSLGTLMTSSYASG---TAFIEMG*VKDIFINEAIYIGKVTYYLCILLKDPLEPHGIS

Parental  QVVPVFQNAKPRLDCLIEVYRSCQEILAHRKA-TSTSP
          QVV.VFQ.AKP.L..L..V...C......RK..TSTSP
Retrocopy QVVTVFQSAKPWLAGLSRV---CSRSWHTRKS<TSTSP

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_844 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003328	1 retrocopy	retro_cpor_815,
Echinops telfairi	ENSETEG00000008623	1 retrocopy	retro_etel_844 ,
Homo sapiens	ENSG00000100564	1 retrocopy	retro_hsap_1506,
Gorilla gorilla	ENSGGOG00000001507	1 retrocopy	retro_ggor_1155,
Macropus eugenii	ENSMEUG00000011325	1 retrocopy	retro_meug_2130,
Myotis lucifugus	ENSMLUG00000004467	1 retrocopy	retro_mluc_910,
Nomascus leucogenys	ENSNLEG00000000739	1 retrocopy	retro_nleu_1747,
Pongo abelii	ENSPPYG00000005925	1 retrocopy	retro_pabe_1255,
Pan troglodytes	ENSPTRG00000006466	1 retrocopy	retro_ptro_1020,
Tarsius syrichta	ENSTSYG00000008465	1 retrocopy	retro_tsyr_1926,