RetrogeneDB ID: retro_smoe_34

Retrocopy location

• Organism: Spikemoss (Selaginella moellendorffii)
• Coordinates: GL377662:546791..547415(+)
• 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_34
CTCTTCAATGAGATGCCAAAGCAAGATGTTTTGTCATATACAAAGATGATATCAGTTTTTTCATCAGGAAATGATTTAGA
AAATGCAAAGGATCTGTTTGATTCTATGCCATTATGAACTGTAGCTGCTTGGAACTCTATGATTATGGCAAATGCTATGA
ATGGGCAAATTGAAAAGGTGGCCATTGTTTTCTTTGAGATGCCCAAGTGGGACTGCTGCTCATGGAATAGCCTCCTGGGT
GCGATCGTGGAGTCTGGGAGGATTAATGATGCAATCATGATGTTTTAGAGAATCCCTTTCAGAGACACAGTTTCATGGAA
CTTGATGATTGCGGCAATGGGTTCTCGCGGTCATATCCACAAGGCGCAAGCTCTCTTTGTCATGATGCTGCAGAGAAATG
CTGTCTCTTGGAGCACAATGATTAGAGCTTAAATGCAGCAGGGACTGGCCGTGGACACAAAGATCGTGTTTGATTCCATG
GAGTCTCATGACACGGTCGCGTGGAACTCACTCCTGGAGGCCTACCTCGTGAGTGCGAGCAATCAAGTGGGCGATGCTAG
GAAAGTGTTTGATTCCATGCCTGATCGAGACCTGGTGTTGTGGACATCAATGATCTCCACCCAT

Alignment

ORF - retro_smoe_34 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.33 %
• Parental protein coverage: 84.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFEKNLVKNLVIWNAAIAAIAATGDLEEAQRLFDGMPFYNFMPW--MMMITMHNGQIEKVAIVFFEIPKW
          .F..............I.......DLE.A..LFD.MP......W..M.M....NGQIEKVAIVFFE.PKW
Retrocopy LFNEMPKQDVLSYTKMISVFSSGNDLENAKDLFDSMPL*TVAAWNSMIMANAMNGQIEKVAIVFFEMPKW

Parental  DCCLWNSLLGTIVESGRIDDAIMMFKRIPFRDIVSWNLMITTMGSCGHIRKAQALFTVMPQRNAVSWSTM
          DCC.WNSLLG.IVESGRI.DAIMMF.RIPFRD.VSWNLMI..MGS.GHI.KAQALF..M.QRNAVSWSTM
Retrocopy DCCSWNSLLGAIVESGRINDAIMMF*RIPFRDTVSWNLMIAAMGSRGHIHKAQALFVMMLQRNAVSWSTM

Parental  IRAYVQQGLAVDAKIMFDSMEPHDMVVYNAMIAA--LASNGHLCKAKILLSKVSESNAVSWNTILTSY
          IRA..QQGLAVD.KI.FDSME.HD.V..N....A...........A............V.W.......
Retrocopy IRA*MQQGLAVDTKIVFDSMESHDTVAWNSLLEAYLVSASNQVGDARKVFDSMPDRDLVLWTSMISTH

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_34 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 ,