RetrogeneDB ID: retro_etel_1987

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321924:37264..37993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000012276
• Aliases: None
• Description: None

Sequence

>retro_etel_1987
GCGTCCCCCTCGTGGAGACTGCAGACCAAGCCAGTCATTACTTGTTTCAAGAGCGTCCTCTTGATCTACACTTTCGTCTT
CTGGATCACTGGTGTTGTCCTTCTTGCTGTTGGCATTTGGGGCAAGGTGAGCCTGGAGAATTATTTTTCCCTTTTAAATG
AAAAGGCCACCAATGTCCCCTTTGTGCTCATTGGCACTGGCACTGTCATTATTCTTTTGGGCACCTTTGGCTGTTTTGCT
ACCTGTCGAGCTTCTGCCTGGATGCTAAAACTGTATGCAATGTTTCTGACCCTAATATTTTTGGTCGAACTGGTTGCTGC
CATCGTAGGATTTGTTTTTAGACATGAGATTAAGAACAACTTTAAGAATAATTATGAGAAAGCTCTGACACAATATAACA
CCACAGGAGATTATAGAAGTGATTCCCTAGACAAGATACAAAATAAATTGCATTGTTGTGGTGTCACCAAATATACAGAT
TGGGAAGATACTAATTATTATGTCCAACACGGATACCCAAAGAGCTGCTGTAAAACTGAATGTACTCCGAACAAAGATGC
AAGTAAAGTAAACCACGAAGGTTGCTTTCTGAAGGTAACGACCACAATAGAGTCAGAAATGGGAATCGTTGCAGGATTTT
CATTTGGCGTTGCTTGCTTTCAGCTGATTGGAATCTTTCTCGCCTACTGCCTTTCTCGTGCCATAACAAATAACCAGTAT
GAGATAGTG

Alignment

ORF - retro_etel_1987 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASPSRRLQTKPVITCFKSVLLIYTFVFWITGVVLLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTVI
          ASPS.RLQTKPVITCFKSVLLIYTFVFWITGVVLLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTVI
Retrocopy ASPSWRLQTKPVITCFKSVLLIYTFVFWITGVVLLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGTVI

Parental  ILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNNFKNNYEKALTQYNTTGDYRS
          ILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNNFKNNYEKALTQYNTTGDYRS
Retrocopy ILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIKNNFKNNYEKALTQYNTTGDYRS

Parental  DALDKIQNKLHCCGVTKYTDWEDTNYYVQHGYPKSCCKTECTPNKDASKVNHEGCFLKVTTTIESEMGIV
          D.LDKIQNKLHCCGVTKYTDWEDTNYYVQHGYPKSCCKTECTPNKDASKVNHEGCFLKVTTTIESEMGIV
Retrocopy DSLDKIQNKLHCCGVTKYTDWEDTNYYVQHGYPKSCCKTECTPNKDASKVNHEGCFLKVTTTIESEMGIV

Parental  AGIFFGVACFQLIGIFLAYCLSRAITNNQYEIV
          AG..FGVACFQLIGIFLAYCLSRAITNNQYEIV
Retrocopy AGFSFGVACFQLIGIFLAYCLSRAITNNQYEIV

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_1987 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987 ,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,