RetrogeneDB ID: retro_eeur_248

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_222573:8769..9543(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSEEUG00000015625
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_eeur_248
CTGAAGGCGCTGATGGCTGCCGCTTGCTGTGTGAGGACCGTGTTCCGGCCAGCCATTCTCAGCTTTGCTTGGGAGGTTTC
GCTTTGCTGTGGGAGCCCACGAAGGAGCTTCATACTACAACACAGTTATCCTCTCTCCTCCAAATACGGTGGGCGGCACA
CCGTGACCATGATTCCCGGCCACGGCATCGGGCCAGAGCTGATGATGCACGTCAAGAACGTGTTCAGGTATCTGAGAGTG
CCTGTGGACTTCGAGGAAGTGATGGTCCGCTCCAGTATTTCCGAAGAGGACGTGTACAACACCGTCATCGCAGTCTGCCG
GAACCGCGTGGCCCTCAAGGGCAACATCGAAACCAACCACAACCTGCCCCCTTCCCACAAATCCTTCAACAACGTGCTTC
GCACCACCCTGGATCTCTTCGCCAACGTCAGCCATTTTAAGAGTCTTCCATGCGTGGAGACCCGACACAAGAACATAGAC
ATCCTGGTGATCCGGGAAAACACAGAGGGCGAGTACAGCAACCTGGAGCACCAGAGTGCGAAAGGAGTGATCGAGAGCCT
CAAGATCATCACAAGGACCAGGTCTTTGCGCATCGCTGAGTACGCCTTCCAGCTGGCCCAGAAGCTGGGACGCAAGAAAG
TCACAGCCGTGCACAAGGCCAACATCATGAAACTGGGAGACGGCCTCTTCCTGCAGTGCTGTAGGGACGTGGCATCCAGT
TACCCCCAGATCTCCTTCGAAGGGATGATTGTGGATAATACCACCATGCAGCTG

Alignment

ORF - retro_eeur_248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKVATAASGAAKAVLRPALLCRPWEXXXXXXXXXXXXXXQQTNPPSAKYGGRHTVTMIPGDGIGPELMLH
          LK...AA......V.RPA.L...WE..............Q...P.S.KYGGRHTVTMIPG.GIGPELM.H
Retrocopy LKALMAAACCVRTVFRPAILSFAWEVSLCCGSPRRSFILQHSYPLSSKYGGRHTVTMIPGHGIGPELMMH

Parental  VKSVFRHACVPVDFEEVHVSSSADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLY
          VK.VFR...VPVDFEEV.V.SS..EED..N...A..RNRVALKGNIETNHNLPPSHKS.NN.LRT.LDL.
Retrocopy VKNVFRYLRVPVDFEEVMVRSSISEEDVYNTVIAVCRNRVALKGNIETNHNLPPSHKSFNNVLRTTLDLF

Parental  ANVIHCKSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAHESG
          ANV.H.KSLP.V.TRH..IDIL..RENTEGEYS.LEH.S..GV.ESLKIIT...SLRIAEYAF.LA...G
Retrocopy ANVSHFKSLPCVETRHKNIDILVIRENTEGEYSNLEHQSAKGVIESLKIITRTRSLRIAEYAFQLAQKLG

Parental  RKKVTAVHKANIMKLGDGLFLQCCKEVAARYPQITFENMIVD-TTMQL
          RKKVTAVHKANIMKLGDGLFLQCC..VA..YPQI.FE.MIVD.TTMQL
Retrocopy RKKVTAVHKANIMKLGDGLFLQCCRDVASSYPQISFEGMIVDNTTMQL

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	0.16 RPM	19.18 RPM
SRP017611_kidney	0.00 RPM	73.33 RPM
SRP017611_liver	0.00 RPM	32.80 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_248 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006029	1 retrocopy	retro_dord_38,
Erinaceus europaeus	ENSEEUG00000015625	1 retrocopy	retro_eeur_248 ,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Oryctolagus cuniculus	ENSOCUG00000016554	1 retrocopy	retro_ocun_80,
Procavia capensis	ENSPCAG00000008973	1 retrocopy	retro_pcap_361,
Pan troglodytes	ENSPTRG00000024398	1 retrocopy	retro_ptro_534,