RetrogeneDB ID: retro_eeur_477

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_320622:4246..5358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSEEUG00000011783
• Aliases: None
• Description: glyoxylate reductase 1 homolog (Arabidopsis) [Source:HGNC Symbol;Acc:24434]

Sequence

>retro_eeur_477
GATCCCACCATCCCCAAGTCCAGCACTATGAAGGGGATGATGGCAGGCCCCATGGCTGCCTTCAAATGGCAGCCACCATG
AGGGAGCCCATTAAAGATGCAGACCCCCATATCCATCACTTTCTGCTCAGCCAAACAGAGACATCAACTGTCTGCTACCA
AGACATCACAAAGAAGTTGAATATCTGCAAAGAGGAGGCAGGGTCCACCTCCATCCAGGCAACAGACAGCACAGCCGTGA
ATGGCAGCATCACATCCACAGACAAAAAGATAGGATTTGGGGGCCTTGGCCTCATGGGAAGTAGCATTGTCTCCAACTTG
CTAAAAATGGGTCACACAGTAACTGTCTAGAATTGGACTGCAGAAAAGTGTGATTTGTTCATCCAGGAGGGGGACCGCCT
AGGAAGAACCCCCGTTGAGGTCGTTTCTACTTGTGATATCACCTTTATCTGCATGTCGAATCCAAAGGCAGCCAAGGATC
TGGTGCTGGGTCCCAGTGGAGTGCTGCAATGCATCCGCCCCGGGAAGTGCTATGTGGACATGTCAACAGTGAACGCTGAC
ACAGTCACCGAGATGGCCCAGGTAATTGTGTCGGGGGGCCACTTTCTGGAAGCCCCGGTCTCAGGGAATCAGCAGCTGTC
TAATGATGGGATGCTGGTGATCTTAGCAGCCAGAGACAGGGGCTTATATGAGGACTGCAGCAGCTGCTTCCAGGCCATGG
GGAAGACCTCCTTCTTTCTAGGTGATGTGGGCAATGCAGCCAAGATGATGCTGATCATGGTCCAAGGGAGCTTCATGGTC
ACCATCGCTGAGGGGCTGACGATGGCCCACCAGACAGGCCAGTCTCAGCAGACACTCATGGACATCTCCAATCAGGGACA
GTTGGCCAGCATCTTCCTGGACCAGAAGAGTCAAAATATCCTGCAAGGCAACTTTAAGCCTGATTTCTACCTGAAGTACA
TTCAGAAGGATCTCTGCTTAACCATCGCGTTGGGTGATGCAGTCAACCACCCCACTCCCATGGCGGCTGCAGGCAATGAG
GTGTATAAAAGAGCCAAGGCACTGGACCAGTCTGACAATGACATGTTTGTCGTGTACTGAACCTATATACAC

Alignment

ORF - retro_eeur_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.93 %
• Parental protein coverage: 74.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLTIPESSTVKGMMAGPMAAFKWQP-TVNEPVKDADPHFHHFLLSQTEKPTVCYQAITKKLKICEEETGS
          D.TIP.SST.KGMMAGPMAAFKWQP.T..EP.KDADPH.HHFLLSQTE..TVCYQ.ITKKL.IC.EE.GS
Retrocopy DPTIPKSSTMKGMMAGPMAAFKWQP<TMREPIKDADPHIHHFLLSQTETSTVCYQDITKKLNICKEEAGS

Parental  TSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQEGARLGRTPA
          TSIQA.DSTAVNGSIT.TDKKIGF.GLGLMGS.IVSNLLKMGHTVTV.N.TAEKCDLFIQEG.RLGRTP.
Retrocopy TSIQATDSTAVNGSITSTDKKIGFGGLGLMGSSIVSNLLKMGHTVTV*NWTAEKCDLFIQEGDRLGRTPV

Parental  EVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDADTVTELAQVIVSRGGRFLEAPVS
          EVVSTCDITF.C.S.PKAAKDLVLGPSGVLQ.IRPGKCYVDMSTV.ADTVTE.AQVIVS.GG.FLEAPVS
Retrocopy EVVSTCDITFICMSNPKAAKDLVLGPSGVLQCIRPGKCYVDMSTVNADTVTEMAQVIVS-GGHFLEAPVS

Parental  GNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGSFMATIAEGLTLA
          GNQQLSNDGMLVILAA.DRGLYEDCSSCFQAMGKTSFFLG.VGNAAKMMLI..MVQGSFM.TIAEGLT.A
Retrocopy GNQQLSNDGMLVILAARDRGLYEDCSSCFQAMGKTSFFLGDVGNAAKMMLI--MVQGSFMVTIAEGLTMA

Parental  QVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYLKYIQKDLGLTIALGDAVNHPTPMGAAAN
          ..TGQSQQTL.DI.NQGQLASIFLDQK.QNILQGNFKPDFYLKYIQKDL.LTIALGDAVNHPTPM.AA.N
Retrocopy HQTGQSQQTLMDISNQGQLASIFLDQKSQNILQGNFKPDFYLKYIQKDLCLTIALGDAVNHPTPMAAAGN

Parental  XVYKRAKALDQSDNDMSAVYRAYIH
          .VYKRAKALDQSDNDM..VY..YIH
Retrocopy EVYKRAKALDQSDNDMFVVY*TYIH

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	3.06 RPM	63.81 RPM
SRP017611_kidney	2.44 RPM	51.57 RPM
SRP017611_liver	0.96 RPM	24.76 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_477 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477 ,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,