RetrogeneDB ID: retro_etel_640

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_12132:790..1571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSETEG00000015797
• Aliases: None
• Description: ribonucleotide reductase M2 [Source:HGNC Symbol;Acc:10452]

Sequence

>retro_etel_640
TTCTGCCGGGGTCCGAGGCTTGTCCGCCATCTGCCCTCGCTTCCCGCCTGCTCCTGTCGCGCACCATGCTCTCCGTCCCC
TTGCGGCTCACCACCATCGACCCCCAGCAGGTCCAGCTTTGGCCCATGAAGGCACTTAGCCTGGGGGACAAGGAGAACAC
GCCCCTGTCCCTCAGCAGCGCCCGCGTCCTGGCCAACCAGGCGGCGAGGAAGATCTTCCAGGAGCCAGAAAGCCCCAAAG
CTCCAGCCTCCAGCATGGAGGACAGCCCTTGCTGAAGGAGAACCCCCGCCGCTTTGTCTTCTTTCCCATCGAGTACCATG
GCATTTGGCAGATGTATAAGAAAGCTGAGGCCTCCTTTTGGACGGCCGAGGGTGGATCTTTCTAAAGACATTCAGCACTG
GGAAGCCCTGCAGCCTGAGGAGAGAGATTTCATATCCCACGCTCTGGCTTTCTTTGCAGCCAGTGACGGCATCGTGCATG
AAAACCTGGTGGAGCGATTTAGCCAAGACATTCAGATTACAGAGGCCCGCTAGTTCTATGGTTTCCAAATTGCAATGGAT
AACATACATTCTGAAATGTATAGTCTCCTGATTGACACTGGCATTGAAGACTCCAAGGAAAGAGGCTATCTCGGTAATGC
CATTGAGATAATGCCGTGTATGAAGAAGGAGACAGATTGGGTTTCCAATGGATCGGGCACAACAAAGCTGCCTGTGGAGA
GTATGTGGTAGTCTTTGCCGCAGGAGGAGGAATCTTCTTTTCTGGTTAGTTCTTTTGCATC

Alignment

ORF - retro_etel_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 84.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FCR-VRGSSPAVRSLPACS-RRTMLSVRVPLATIDPQQVQLSPLKALSLADKENTPPSLSSARVLASKAA
          FCR.VRG.S......P.....RTMLSV...L.TIDPQQVQL.P.KALSL.DKENTP.SLSSARVLA..AA
Retrocopy FCR>VRGLSAICPRFPPAP>SRTMLSVPLRLTTIDPQQVQLWPMKALSLGDKENTPLSLSSARVLANQAA

Parental  RKIFQEP-SPRAPASSVEDEPLLKENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALK
          RKIFQEP.SP.APASS.ED.P.....P.....FP...........K....F.....VDLSKDIQHWEAL.
Retrocopy RKIFQEPESPKAPASSMEDSPC*RRTPAALSSFPSSTMAFGRCIRKLRPPFGRPR-VDLSKDIQHWEALQ

Parental  PEERYFISHVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKER
          PEER.FISH.LAFFAASDGIV.ENLVERFSQ..QITEAR.FYGFQIAM.NIHSEMYSLLIDT.I.DSKER
Retrocopy PEERDFISHALAFFAASDGIVHENLVERFSQDIQITEAR*FYGFQIAMDNIHSEMYSLLIDTGIEDSKER

Parental  EYLFNAIETMPCVKKKADW-ALRWIGDKEATYGERVVAFAAVEGIFFSGSFASI
          .YL.NAIE.MPC.KK..DW....WIG...A..GE.VV.FAA..GIFFSG.F..I
Retrocopy GYLGNAIEIMPCMKKETDW<GFQWIGHNKAACGEYVVVFAAGGGIFFSG*FFCI

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_640 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 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640 , retro_etel_691,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,