RetrogeneDB ID: retro_eeur_316

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_251742:3936..5252(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSEEUG00000006324
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_eeur_316
ATCTTGGAGAGCAAGATAAATCTCAGAACTCATTATAAAGAACAACAAGGAACATTATGTGGTCTGAAAGTGAGAACCAA
GATATGGCATTGAGCTTCCAGTTTGAAGCAAGTTGTCAAGAGATCTGGGACGACATTTGCCATATTCAAGGTACAGGTTC
CTGCGTCGAAATCACACACGATTTCTTAGAGGAATCACTAGAGCAATATCCTGAAGTGCTGGAAACCAGTACTATGGTTG
ACTTGCCTAACTGTGAACTTGATAAACTTCAACAAATTTCTGATTTAATTACCTCAGTTCTCACCTCACCTATCCTTAAG
GAAAGGCTGGCTTTAGCCTTAGAAAATAAGGACTATATAAAAAGTCTACTACATCTGTTTCATATTTGCGAAGACAGAAA
GGACACCAAAGGCTTGGGTCATCTGCATGAAATTATTAAAGGAATTATGTATCTCAACAAGACCACTTTGTTTGAGATCA
TGTTATCTGATAAGTATATTATGGACGTGGTGGGATGCCTTGAATATGACCCTTCTTTGGATCAACCAAAAAATCATAGA
GAATTCTTGACACAAAATGTAAAGTTCAAGGAAGTTATACCAAAAACAGATTGTGCACTTAAGCGAAAAATACATCAGAC
CTATAGAATGCAGTACATTCACGATATTCTTTCGCCTACATCACCAGTATTTGAAGATAATTTTATCTCTACTCTTAAAA
CTTTCATTTTCTATAACAAGGTTGAAATAATCTGCTTGCTACAAGATGATGATGTGTTTTTGTCTGGCATTTTCACACAG
TTAATGGATAAGACTACAGACTGTAACAAACTGTGTGAAATGGTATTGTTTGTCAAGGAATTTTGTTCATTTTCTCAGAC
ATTACAGCCTCACAATAAGGATAGACTATTCAAAACCTTGACACAATTGAAAATTCTTCCAGCTCTTAAAAGTGTAATGA
GTGTGAATGATGTGCAAATAAGGTCAGCTTCTGCTGATATATTTGGTTTTCTAGTGGAGTATAGTCCATGCATGATCCGG
AGGTTTGTGTTGGAAGATGCTCAACAGAGTAAAGGCAGTGATCTTTTCATTAATTTAGTTATTGACCAGATCATCAGGGA
TACTGATCCTGAACTAGGAGGTGCTATTCAGTTAACAGGACTTCTTCGTACTCTTCTTGACCCAGAGAACATGCAAATAA
CACCTAGTAGGTATGAAAGAAATGAATTTCAGAATTTCTTCTATAAACACTGTCTGCATAACCTCATAGCACCACTTTTA
GCTACCACTACAGAAGATATATATGAAAAGGATAAT

Alignment

ORF - retro_eeur_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.37 %
• Parental protein coverage: 66.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLESKINPNTAYQKQQDTL-IVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEE
          .LESKIN..T.Y.K.Q....I.WSE.EN.D.ALSFQ..A.C.EIW..IC..QG....V.IT.D...ES.E
Retrocopy ILESKINLRTHY-KEQQGT<IMWSESENQDMALSFQFEASCQEIWDDICHIQGTGSCVEITHDFLEESLE

Parental  ERFDDM-SSPGLELPSCELSRLEEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEG
          ........S....LP.CEL..L..I..L..S.L.SP...E.LALALEN..YIK.LL.LFH.CED.....G
Retrocopy QYPEVLETSTMVDLPNCELDKLQQISDLITSVLTSPILKERLALALENKDYIKSLLHLFHICEDRKDTKG

Parental  LHHLYEIIKGIFLLNRTALFEVMFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELK
          L.HL.EIIKGI..LN.T.LFE.M.S...IMDV.GCLEYDP.L.QP..HREFLT...KFKEVIP..D..LK
Retrocopy LGHLHEIIKGIMYLNKTTLFEIMLSDKYIMDVVGCLEYDPSLDQPKNHREFLTQNVKFKEVIPKTDCALK

Parental  QKIHQTYRVQYIQDMVLPTPSVFEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDESTDEEKR
          .KIHQTYR.QYI.D...PT..VFE.N..STL..FIF.NKVEI...LQ.D..FL...F.QL.D..TD..K.
Retrocopy RKIHQTYRMQYIHDILSPTSPVFEDNFISTLKTFIFYNKVEIICLLQDDDVFLSGIFTQLMDKTTDCNKL

Parental  QELVNFLKEFCAFSQTLQPQNRDAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSMVRE
          .E.V.F.KEFC.FSQTLQP.N.D..FKTL....ILPAL.......D.Q.RSA..DIF..LVEY.P.M.R.
Retrocopy CEMVLFVKEFCSFSQTLQPHNKDRLFKTLTQLKILPALKSVMSVNDVQIRSASADIFGFLVEYSPCMIRR

Parental  FVMQEAQQNDDDILLINLIIEHMICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHC
          FV...AQQ.....L.INL.I...I.DTDPELGGA.QL.GLLRTL.DPENM..T....E..EF..FFYKHC
Retrocopy FVLEDAQQSKGSDLFINLVIDQIIRDTDPELGGAIQLTGLLRTLLDPENMQITPSRYERNEFQNFFYKHC

Parental  MHVLTAPLLANTTEEKPSKDD
          .H.L.APLLA.TTE....KD.
Retrocopy LHNLIAPLLATTTEDIYEKDN

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	0.00 RPM	56.08 RPM
SRP017611_kidney	0.00 RPM	62.83 RPM
SRP017611_liver	0.00 RPM	28.94 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_316 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	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316 ,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,