RetrogeneDB ID: retro_eeur_15

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_371041:4698..6252(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000015299
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSEEUG00000012262
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_eeur_15
ATGCTGCACTTCCTGGTGCCCCGGCTGCTCTGCCTGGGCGGCCGGTCCGCCCGGTACTCCTCTGCAGCGGCCCTCCCGAA
ACCCATCCCTAAGCCCGACATCCGCTACAGCCAGCTCTTCATTAACAACGAGTGGCGCGATGCAGTCAGTAAGAAGACCT
TCCCCACCGTCAACCCCAGCACGGGCGACGTCATCGGGCACGTGGCCGAAGGAGACCGGGCTGACGTGGACCTGGCAGTG
AAAGCCGCCCGGGAGGCCTTCCGCCTGGGGTCTCCGTGGCGTCGGATGGACGCCTCCGAGCGGGGCCGGCTGCTGAACCG
CCTGGCCGACCTGGTGGAGCGGGATCGCGTCTACTTGGCCTCACTGGAGACCTTAGACAACGGGAAGCCCTTCCAGGAGT
CTTACGTCTTGGACCTGGATGAGGTCATCAAGGTGTACCGGTACTTTGCCGGCTGGGCTGACAAGTGGCACGGCAAGACC
ATCCCCATGGATGGCGAGCACTTCTGCTTCACCCGGCATGAGCCTGTGGGTGTCTGTGGCCAGATCATCCCGTGGAATTT
CCCCTTGGTCATGCAGGGCTGGAAGCTGGCCCCCGCCCTTGCCACGGGCAACACGGTGGTCATGAAGGTGGCCGAACAGA
CACCCCTCTCTGCCCTGTACCTGGCCTCCCTCATCAAAGAGGCAGGCTTCCCGCCAGGGGTGGTGAACATCATCACTGGC
TACGGCCCCACGGCAGGAGCAGCCATCGCCCAGCACATGGACATCGACAAAGTCGCCTTCACGGGCTCCACCGAGGTGGG
CCACCTGATCCAGAAGGCGGCCGGCGACTCCAACCTCAAGAGGGTCACCCTGGAGCTGGGTGGGAAGAGCCCCAGCATTG
TGTTGGCCGACGCGGATATGGACCACGCCGTGGAGCAGTGCCACGAAGCCCTCTTCTTCAACATGGGCCAGTGCTGCTGC
GCCGGCTCCCGCACCTTCGTGGAAGAGTCCATCTATGATGAGTTTCTGGAGAGGACCGTGGAGAAAGCCAGGCAGAGGAA
AGTGGGCAATCCCTTTGAGCTGGACACCCAACAGGGGCCCCAGGTAGACAAGGAGCAGTTTGAACGAATCCTGGGCTACA
TTCGGCTGGGTCAGAAAGAGGGTGCGATGCTTCTCTGTGGTGGGGAGCGTTTCGGGGAGCGGGGCTTCTTCATCAAGCCC
ACTGTCTTTGGGGGTGTGCAGGATGACATGAGGATTGCCAGAGAGGAGATCTTTGGGCCCGTGCAGCCCTTGTTCAAGTT
CAAGAAAATAGAGGAGGTTATTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCTGCCGTGTTTACCCGGGATCTGG
ATAAGGCCTTGTACTTCACACAGGCCCTCCAAGCTGGGACGGTGTGGGTGAACACCTACAACATCGTCACCTGTCACACA
CCATTTGGGGGCTTTAAGGAATCAGGCAATGGGAGGGAGTTGGGGGAGGATGGGCTCAAGGCCTACACAGAGGTAAAGAC
GGTCACCATCAAGGTTCCACAGAAGAACTCGTAA

Alignment

ORF - retro_eeur_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFINNEWQNSESGRVFPVYNPATGEQVCEVQEADKADIDKAVQAARLAFSLGSVWRRMDASERGRLLDKL
          .FINNEW....S...FP..NP.TG.....V.E.D.AD.D.AV.AAR.AF.LGS.WRRMDASERGRLL..L
Retrocopy LFINNEWRDAVSKKTFPTVNPSTGDVIGHVAEGDRADVDLAVKAAREAFRLGSPWRRMDASERGRLLNRL

Parental  ADLVERDRAILATMESLNGGKPFLQAFYVDLQGVIKTLRYHAGWADKIHGMTIPVDGDYFTFTRHEPVGV
          ADLVERDR..LA..E.L..GKPF......DL..VIK..RY.AGWADK.HG.TIP.DG..F.FTRHEPVGV
Retrocopy ADLVERDRVYLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKWHGKTIPMDGEHFCFTRHEPVGV

Parental  CGQIIPWNFPLLMFAWKIAPALCCGNTIVIKPAEQTPLSALYMGALIKEAGFPPGVINILPGYGPTAGAA
          CGQIIPWNFPL.M..WK.APAL..GNT.V.K.AEQTPLSALY...LIKEAGFPPGV.NI..GYGPTAGAA
Retrocopy CGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAA

Parental  IASHVGIDKIAFTGSTEVGKLVQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQC
          IA.H..IDK.AFTGSTEVG.L.Q.AAG.SNLKRVTLELGGKSP.I..ADAD.D.AVEQ.H...FFN.GQC
Retrocopy IAQHMDIDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADADMDHAVEQCHEALFFNMGQC

Parental  CTAGSRIFVEESIYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGG
          C.AGSR.FVEESIY.EF..R.VE.A..R.VG.PF...T.QGPQ.DK.Q...IL..I..G..EGA.L.CGG
Retrocopy CCAGSRTFVEESIYDEFLERTVEKARQRKVGNPFELDTQQGPQVDKEQFERILGYIRLGQKEGAMLLCGG

Parental  KGLGCKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALT
          ...G..GFFI.PTVF..V.DDMRIA.EEIFGPVQ....FK...EVIERANN...GL.AAVFT.D..KAL.
Retrocopy ERFGERGFFIKPTVFGGVQDDMRIAREEIFGPVQPLFKFKKIEEVIERANNTRYGLAAAVFTRDLDKALY

Parental  VSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGRE
          ...A.QAGTVW.N.YN......PFGGFK.SGNGRE
Retrocopy FTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRE

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	0.32 RPM	10.47 RPM
SRP017611_kidney	112.71 RPM	5.06 RPM
SRP017611_liver	36.17 RPM	0.48 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_15 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
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106,
Erinaceus europaeus	ENSEEUG00000012262	1 retrocopy	retro_eeur_15 ,
Monodelphis domestica	ENSMODG00000008641	1 retrocopy	retro_mdom_254,
Pan troglodytes	ENSPTRG00000007113	1 retrocopy	retro_ptro_118,
Sorex araneus	ENSSARG00000012720	1 retrocopy	retro_sara_40,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111,
Tarsius syrichta	ENSTSYG00000004549	1 retrocopy	retro_tsyr_8,
Tursiops truncatus	ENSTTRG00000002361	1 retrocopy	retro_ttru_932,