RetrogeneDB ID: retro_smoe_12

Retrocopy location

• Organism: Spikemoss (Selaginella moellendorffii)
• Coordinates: GL377578:1474402..1475038(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: SELMODRAFT_79606
• Aliases: None
• Description: None

Sequence

>retro_smoe_12
CTCTTCAATGAGACGCTAGAGCAAGGTGTTTTGTTATATACAATAATGATATCACTTTTAGCATCAAGAAGTGATTTAGA
AAATGTGAAGGATCTATTTTATTTTATGCCATTACGAACTGTAGCCACTTGGAACTCTTTAATTATGGCAAATGCCGAAA
ATGGGCAAATTGAAAAGGTGGCCATTGTTTTCTTTGAGATGCTCAAATGGGACTGCTGCTCATGGAATAGCCTCCTGGGC
ACGATCGTAGAGTCTGGGAGGATTGACAATGCAATCATGATGTTTCAGAGAATCCCTTTCAGAGACACAGTTTCATGGAA
CCTGATGATTGTGGCAATGGGTTCTCATGGCCATATCTGTGAGGTGCAAGCTCTCTTTTTTGTGATGCTGCAAAGAAACA
CTGTCTTTTGGAGCACAATGATCGGAGCTTACGCACAGTAGGGACTGGCCATGGATGCAAAGATCATGTTTGATTCCATG
GAGTCTCACAACACGGTCACATGGAACTCACTCCTGGCAGCCTACCTCGTGAGCAATCCAGTGGGCAATGCTAGAAAAGT
GTTTGATTCCATGCCTCATTGAGATATGGTGTCGTGGACGTTGATGATCTCCACCCACACCGCACAGGGCCAGATG

Alignment

ORF - retro_smoe_12 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.36 %
• Parental protein coverage: 86.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFEKNLVKNLVIWNAAIAAIAATGDLEEAQRLFDGMPFYNFMPW--MMMITMHNGQIEKVAIVFFEIPKW
          .F...L..........I...A...DLE....LF..MP......W....M....NGQIEKVAIVFFE..KW
Retrocopy LFNETLEQGVLLYTIMISLLASRSDLENVKDLFYFMPLRTVATWNSLIMANAENGQIEKVAIVFFEMLKW

Parental  DCCLWNSLLGTIVESGRIDDAIMMFKRIPFRDIVSWNLMITTMGSCGHIRKAQALFTVMPQRNAVSWSTM
          DCC.WNSLLGTIVESGRID.AIMMF.RIPFRD.VSWNLMI..MGS.GHI...QALF.VM.QRN.V.WSTM
Retrocopy DCCSWNSLLGTIVESGRIDNAIMMFQRIPFRDTVSWNLMIVAMGSHGHICEVQALFFVMLQRNTVFWSTM

Parental  IRAYVQQGLAVDAKIMFDSMEPHDMVVYNAMIAALASNGHLCKAKILLSKVSESNAVSWNTILTSYIHFG
          I.AY.Q.GLA.DAKIMFDSME.H..V..N...AA.........A............VSW..........G
Retrocopy IGAYAQ*GLAMDAKIMFDSMESHNTVTWNSLLAAYLVSNPVGNARKVFDSMPH*DMVSWTLMISTHTAQG

Parental  HL
          ..
Retrocopy QM

Legend:

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

Expression

RNA-Seq

Selaginella moellendorffii was not studied using RNA-Seq expression data.

ChIP-Seq

Selaginella moellendorffii was not studied using ChIP-Seq data.

EST

Selaginella moellendorffii was not studied using EST data.

TSS

Selaginella moellendorffii was not studied using FANTOM5 data.

Lab

retro_smoe_12 was not experimentally validated.

Homology

Retrocopy orthology:

Selaginella moellendorffii 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Selaginella moellendorffii	SELMODRAFT_79606	2 retrocopies	retro_smoe_12 , retro_smoe_34,