RetrogeneDB ID: retro_sara_40

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_210189:1941..3495(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000014569
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSSARG00000012720
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_sara_40
ATGCTGCGCTCCCTGCTGCCCCGGCTGCTTAGCCTGCGTGCCAGGACGGCCCCGTACTCGTCAGCCGCGGCCCTGCCCAA
GCCCATCCCGAACCCAGACATCCGCTACAACCAGCTCTTCATCAACAACGAGTGGCAAGATGCTGCCAGCAAGAAGACCT
TCCCCACCATCAACCCGTCCACGGGAGAGGTGCTGGGCCACGTGGCTGAAGGGGACCGGGCGGACGTGGACCGGGCAGTG
AAAGCGGCCCGGGAGGCCTTCCGCCTGGGCTCTCCGTGGCGCCGGATGGATGCCTCAGAGCGGGGCCGGCTGCTCAACCG
CCTGGCGGACCTGGTGGAGCGGGACCGGGTATACCTGGCCTCCCTGGAGACCCTGGACAACGGCAAGCCCTTCCAGGAGT
CCTACGTCATGGACCTGGACGAGGTCATCAAGGTGTACCGGTACTTCGCTGGCTGGGCTGACAAGTGGCACGGCAAGACC
ATCCCCATGGACGGCGAGCACTTCTGCTTCACCCGGCACGAGCCCGTGGGCGTCTGTGGCCAGATCATCCCCTGGAACTT
CCCGCTGGTCATGCAGGGCTGGAAGCTCGCCCCGGCGCTCGCCACGGGCAACACGGTAGTGATGAAGGTGGCGGAGCAGA
CGCCCCTGTCCGCCCTCTACTTGGCCTCCCTCATCAAAGAGGCCGGCTTCCCCCCCGGGGTGGTGAACATCATCACCGGC
TACGGCCCCACGGCCGGCGCGGCCATTGCCCAGCACATGGACGTAGACAAAGTGGCCTTCACCGGCTCCACGGAGGTGGG
CCACCTGATCCAGAAGGCGGCGGGGGACTCCAACCTCAAGCGCGTCACGCTGGAGCTGGGCGGGAAGAGCCCCAGCATCG
TGCTGGCCGACGCCGACATGGACCACGCCGTGGAGCAGTGCCACGAGGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGC
GCCGGCTCCCGCACCTTCGTCCAGGACTCCATCTACGACGAGTTCCTCGAGAGGACCGTGGAGAAGGCGAAGCAGAGGAA
AGTGGGGAACCCCTTTGAGCTGGACACCCGCCAGGGCCCCCAGGTGGACCAGGAGCAGTTCGACCGCATCCTGGGCTACA
TCAAGCTGGGCCAGAAGGAGGGGGCCAAGCTCATGTGTGGCGGGGAGCGCTTTGGGGAGCGCGGCTTCTTCATCAAGCCC
ACCGTCTTCGGGGGCGTGCAGGACGACATGCGGATCGCCAAGGAGGAGATCTTCGGGCCCGTGCAGCCCTTGTTCAAGTT
CAAGAAGATCGAGGAGGTGATCGAGAGGGCCAACAACACCAGGTACGGCCTGGCGGCTGCCATATTCACCCAGGACCTGG
ACAAAGCCTTGTACTTCACACAGGCGCTGCAGGCCGGCACCGTGTGGGTGAACACCTACAACATCGTCACCGCACAGACG
CCCTTCGGGGGCTTCAAGGAATCTGGCAGTGGGAGGGAGCTGGGGGAGGACGGGCTGAAGGCTTACACCGAGGTCAAGAC
CGTCACCATCAAGGTCCCCCAGAAGAACTCCTAA

Alignment

ORF - retro_sara_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMESLNGGKPFLQAFYVDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGVCGQIIPWNFPLL
          ..E.L..GKPF......DL..VIK..RY.AGWADK.HG.TIP.DG..F.FTRHEP.GVCGQIIPWNFPL.
Retrocopy SLETLDNGKPFQESYVMDLDEVIKVYRYFAGWADKWHGKTIPMDGEHFCFTRHEPVGVCGQIIPWNFPLV

Parental  MFAWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVINILPGYGPTAGAAIASHTGIDKIAF
          M..WK.APAL..GNTVV.K.AEQTPLSALY...LIKEAGFPPGV.NI..GYGPTAGAAIA.H...DK.AF
Retrocopy MQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAF

Parental  TGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQCCTAGSRIFVEES
          TGSTEVG.LIQ.AAG.SNLKRVTLELGGKSP.I..ADAD.D.AVEQ.H...FFN.GQCC.AGSR.FV..S
Retrocopy TGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADADMDHAVEQCHEALFFNMGQCCCAGSRTFVQDS

Parental  IYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYIRILELIQSGVAEGPKLECGGKGLGRKGFFIEP
          IY.EF..R.VE.AK.R.VG.PF...T.QGPQ.D..Q..RIL..I..G..EG.KL.CGG...G..GFFI.P
Retrocopy IYDEFLERTVEKAKQRKVGNPFELDTRQGPQVDQEQFDRILGYIKLGQKEGAKLMCGGERFGERGFFIKP

Parental  TVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSEFGLVAAVFTNDINKALTVSSAMQAGTVWI
          TVF..V.DDMRIAKEEIFGPVQ....FK...EVIERANN...GL.AA.FT.D..KAL....A.QAGTVW.
Retrocopy TVFGGVQDDMRIAKEEIFGPVQPLFKFKKIEEVIERANNTRYGLAAAIFTQDLDKALYFTQALQAGTVWV

Parental  NCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEIKTVTVKIPQKNS
          N.YN...AQ.PFGGFK.SG.GRE.GE.GL..Y.E.KTVT.K.PQKNS
Retrocopy NTYNIVTAQTPFGGFKESGSGRELGEDGLKAYTEVKTVTIKVPQKNS

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_40 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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,