RetrogeneDB ID: retro_eeur_663

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_377860:95171..96378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA3
• Ensembl ID: ENSEEUG00000005430
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 3 [Source:HGNC Symbol;Acc:12470]

Sequence

>retro_eeur_663
TCTCTCCAGTTTTTGTTAGATGCTTGTAAAATTCTAGTCAATGGAGCAGGCGGCTTAGGATATGAGCTCCTGAAAAATCT
GGCATTATCTGGTTTTAGACAGATTCATGTTATAGATATGGACACTATAGATGTTTCCAATTTAAATAGGCAGTTTTTAT
TTAGGCCCAAAGATGTTGGAAGACCTAAAGCAGAAGTTGCTGCAGAATTTCTAAATGATTGAATTCCTAATTGCAACGTA
GTTCCACATTTCAACAAGATTCAAGATTTTAATGATACTTTCTATTGACAATTCCATATAATTGTATGTGGGCTGGACTC
TTATCATAGCCAGAAGGTGGATAAATGGCATGTTGATATCTCTTCTAAATTACGAACATGGTGTATTAGATCCAAGCTCC
ATAGTCCCTTTGATAGACAGGGGGACCGAAGGTTTTAAAGGAAATGCCCAAGTTATTCTGCCTGGAATGACTGCTTGCAT
TGAATGCACACTGGAACTGTATCTGCCACAGGTTAGTTTTCCCATGTGTACCATTGTGTCTATGCCCAGACTACCAGAAC
ACTGTATTGAGTATGTAAGGATACTGCAGTGGCCTAAGGAGCAGCCTTTTGGAGAAGGGGTTCCATTAGATGGAGATGAT
CCTGATCATATTCAGTGGATTTTTCAAAAATCACTAGAAAGAGCATCACAATATAACATTAGAGGTGTTACATATAGACT
CACTCAGGGTGTAGTAAAACAAATCATACCTGCAGTAGCTTCCACAAATGCTGTCATTGCAGCTGTCTGTGCCACTGAGG
TTTTTAAAATAGCCACAAGTGCATATATTCCCCTTAATAACTACTTGGTATTTAATGATGTAGATGGACTCTACACATAC
ACATTTGAAGCAGAGAGAAAGGACAACTGCCCAGCCTGTAGCCAGCTTCCTCAAAATATTCAGTTTTCTTCATCAGCTAA
ACTGCAGGAAGTTTTAGATTACCTAACCAATAGTGCTTCTCTGCAGATGAAATCTCCAGCCATCACAGCCACATTAGAGG
GGAAGAATAGGACACTTTACTTACAGTCGGTAACTTCTATTGAAGAAAGAACAAGACCAAATCTCTCCAAGACACTGAAA
GAATTGAGACTTGTCGACAGGCAAGAATTGGCAGTTGCTGATGTCACCACACCACAGACTGTACTATTCAAACTTCATTT
TACTTCT

Alignment

ORF - retro_eeur_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 88.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDVGRPKAEVAAEF
          SLQFLLD.CK.LV.GAGGLG.ELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDVGRPKAEVAAEF
Retrocopy SLQFLLDACKILVNGAGGLGYELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDVGRPKAEVAAEF

Parental  LNDRIPNCNVVPXXXXXXXXXXXXXXXFHIIVCGLDS-IIARRWINGMLISLLNYEDGVLDPSSIVPLID
          LND.IPNCNVVP...............FHIIVCGLDS.IIARRWINGMLISLLNYE.GVLDPSSIVPLID
Retrocopy LND*IPNCNVVPHFNKIQDFNDTFY*QFHIIVCGLDS>IIARRWINGMLISLLNYEHGVLDPSSIVPLID

Parental  GGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRILQWPKEQPFGXXXXX
          .GTEGFKGNA.VILPGMTACIECTLELY.PQV.FPMCTI.SMPRLPEHCIEYVRILQWPKEQPFG.....
Retrocopy RGTEGFKGNAQVILPGMTACIECTLELYLPQVSFPMCTIVSMPRLPEHCIEYVRILQWPKEQPFGEGVPL

Parental  XXXXXXXXXXXXPKSLERASQY-IRGVTYRLTQGVVKRIIPAVASTNAVIAXXXXXXXXXXXXXAYIPLN
          .............KSLERASQY.IRGVTYRLTQGVVK.IIPAVASTNAVIA.............AYIPLN
Retrocopy DGDDPDHIQWIFQKSLERASQYNIRGVTYRLTQGVVKQIIPAVASTNAVIAAVCATEVFKIATSAYIPLN

Parental  NYLVFNDVDGLYTYTFEAERKDNCPACSQLPQNIQFSSSAKLQEVLDYLTNSASLQMKSPAITATLEGKN
          NYLVFNDVDGLYTYTFEAERKDNCPACSQLPQNIQFSSSAKLQEVLDYLTNSASLQMKSPAITATLEGKN
Retrocopy NYLVFNDVDGLYTYTFEAERKDNCPACSQLPQNIQFSSSAKLQEVLDYLTNSASLQMKSPAITATLEGKN

Parental  RTLYLQSVTSIEERTRPNLSKXXXXLGLVDGQELAVADVTTPQTVLFKLHFTS
          RTLYLQSVTSIEERTRPNLSK....L.LVD.QELAVADVTTPQTVLFKLHFTS
Retrocopy RTLYLQSVTSIEERTRPNLSKTLKELRLVDRQELAVADVTTPQTVLFKLHFTS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	23.20 RPM	28.52 RPM
SRP017611_kidney	20.82 RPM	19.69 RPM
SRP017611_liver	7.07 RPM	6.91 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_663 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663 ,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,