RetrogeneDB ID: retro_etel_1385

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_257374:489..1090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSETEG00000007930
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_etel_1385
GCTGTGGTTCCTGGCCCCGCAGAGCACCCCCTGCAATACAACTACACTTTCTGGTACTCCAGGAGGACCCCCGGCCGGCC
CACCAGCTCACAGAGCTACGAGCAGAACATTAAGCAGATGGCACCTTTGCCTCGGTGGAGCAGTTCTGGAGGGTTTACAG
CCACATGGTACGTCCCGGGGACCTGATCGGCCACAGTGACTTCCACCTCTTCAAGGAAGGGATCAAGCCCATGTGGGAGG
ATGATGCAAATAAGAACGGTGGCAAGTGGATCATTCGGCTGCGGAAGGGCTTGGCGTCGCGCTGCTGGGAGAACCTCGTC
CTGGCCATGCTGGGAGAGCAATTCTTGGTTGGGGAGATCTGTGGGGCTGTGGTCTCTGTCCGGTTTCAGGAGGACATCAT
CTCCATCTGGAACAAGACTGCCAGTGACCAAGCTACCACAGCTCGAATCCGGGACACGCTCCGCCTCGTGCTGAACCTAC
CTCCCAACACCATCATGGAGTACAAAACCCACACCGACAGCATCAAAATGCCAGGCAGGCTGGGCCCCCAAAGGCTCCCT
TTTCAAAACCTCTGGAAGACGCGGGTGTACGTGCCATGAGC

Alignment

ORF - retro_etel_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.63 %
• Parental protein coverage: 79.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQI-GTFASVEQFWRVYSHMVRPGDLTGHSDFH
          AVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQ..GTFASVEQFWRVYSHMVRPGDL.GHSDFH
Retrocopy AVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQM<GTFASVEQFWRVYSHMVRPGDLIGHSDFH

Parental  LFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLVLAMLGEQFMVGEEICGAVVSVRFQEDIISIWN
          LFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLVLAMLGEQF.VGE.ICGAVVSVRFQEDIISIWN
Retrocopy LFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLVLAMLGEQFLVGE-ICGAVVSVRFQEDIISIWN

Parental  KTASDQATTARIRDTLRRVLNLPPNTIMEYNTHTDSIKMPGRL-GPQRL-FSKPLEDAGERAMS
          KTASDQATTARIRDTLR.VLNLPPNTIMEY.THTDSIKMPGRL.GP....FSKPLEDAG.RAMS
Retrocopy KTASDQATTARIRDTLRLVLNLPPNTIMEYKTHTDSIKMPGRL<GPPKAPFSKPLEDAGVRAMS

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_1385 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963, retro_chof_369, retro_chof_567,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Echinops telfairi	ENSETEG00000007347	3 retrocopies	retro_etel_1285, retro_etel_1449, retro_etel_499,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385 ,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,