RetrogeneDB ID: retro_etel_1219

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_230416:965..1561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2B
• Ensembl ID: ENSETEG00000020338
• Aliases: None
• Description: ribonucleotide reductase M2 B (TP53 inducible) [Source:HGNC Symbol;Acc:17296]

Sequence

>retro_etel_1219
GATGAGCCCTGATTGCAGTAGAACCCCGGCCAACTTTGTTGTCTTTCCCATGGAGTACCATGACCATTTGGCAGATGTAT
AAGAAAAGCTGAAGCCTCCTTTTTGGACGAGCCGAAGAAGCTGGATCTTTCTAAAGCCACTCCAGCACTGGGAAGCCCTG
AAGCATGAGGAGAGAGATTTCATATCCCACGCTCTGGCTTTCTTTGCAACCAGTGATGCATAGTGCATGAGAACCTAGTG
GAGCGATTTAGCCAAGAAGTTCAGATTACAGAGGCCCGTTGTTTCTATAGCTTCCAAATTGCTATGGAAAACATACATTC
TGAAATGTATAGTCTCCTGATTGACACATTAAAGATTCCAAGGAAAGGGAGTATCTCTTCAATGTCATTGAGACAATGCC
TTGTGTGAAGAAGAAGGCAGATTGGGCCTTGCGTTGGATTGGCGACAAAGAAGCTACCTACGGAGAGCGAGTTGTAGCCT
TTGCAGCAGTGGAAGGCATCTTCTTCTCCGGTTCGTTTGCATCCATCTTCTGGCTCAAGAAACGAGGACTAATGCCAGGC
CTCACGTTTTCCAAGGAACTTATTAGCAGAGATGAG

Alignment

ORF - retro_etel_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 56.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DEPLLR-KSSRRFVIFPIQYPD-IWKMYKQ-AQASFWTA-EEVDLSKDLP-HWNKLKSNEKCFISHILAF
          DEP.L.......FV.FP..Y.D.IW.MYK..A.ASF.......DLSK..P.HW..LK..E..FISH.LAF
Retrocopy DEP*LQ>RTPANFVVFPMEYHD>IWQMYKK>AEASFLDEPKKLDLSKATP>HWEALKHEERDFISHALAF

Parental  FAASDG-IVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDAYIRDPKK-REFLFNAIETMP
          FA.SD..IV.ENLVERFSQEVQ..EARCFY.FQI..EN.HSEMYSLLID.....P.K.RE.LFN.IETMP
Retrocopy FATSDA<IVHENLVERFSQEVQITEARCFYSFQIAMENIHSEMYSLLIDT-LKIPRK<REYLFNVIETMP

Parental  CVKKKADWALRWIADRKSTFGERVVAFAAVEGIFFSGSFAAIFWLKKRGLLPGLTFSNELISRDE
          CVKKKADWALRWI.D...T.GERVVAFAAVEGIFFSGSFA.IFWLKKRGL.PGLTFS.ELISRDE
Retrocopy CVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSKELISRDE

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_1219 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118, retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219 ,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555, retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,