RetrogeneDB ID: retro_smoe_20

Retrocopy location

• Organism: Spikemoss (Selaginella moellendorffii)
• Coordinates: GL377603:377439..378099(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: SELMODRAFT_20534
• Aliases: None
• Description: None

Sequence

>retro_smoe_20
CTCGTGTCGTGGAATTCCATTCTTGCGGCATATGCCCGGAACGGGCATGTAGAGGGAGTCGAACGTGTTTTTGATTCTAT
GGAGGCTCGTGACCTTGTGTCATGGACGACAATCTTGGTTGCCTTGTCGCAGGGCGGAGATTTGCACGGAGCAAAGCTTT
TGTTTGATGCAATGCCGCAGCACGATCTCGTTGCCTGGACCGCGATGCTCGGCGCATACGCACTGAACGAGGATGTCGAT
TCGGCACAGAGGATTTTCCGCGAGATGCCTGAGATAGATCTCGTTTCGTGCAACACCGTGATGCGATGCTGCCGTGATGC
TAGACAATCAAAGCTTATATTTGACTCCATGCCGCAGAGAGCTCTCTCGTCGTGGACAACAATGCTCGCTGTTCTTGCCA
AGAACAGCCCCGGGGAGGAAACCAAGAGCTTTTTCTATCAAATGCTGGAGCTTGATCTTACTTCCTGTATGATAATGTTT
CTCTCACAACCCTCAGACTTGGAGCTTGTGAAGGCCACCTTTGATCAAATTCCGCAGCGGGATCTGTGCTCTTGGAACTC
TGTTCTTTCGGCGTATGCCCAATGAGGGCATTGTGACTTTGGTTTAAGACTCTTTAACAAGATGCCCGAAATGGATATGG
TTTCGTGGAACACAATGTTA

Alignment

ORF - retro_smoe_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVSWNSILTAYARKGH-EREKRVFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAML
          LVSWNSIL.AYAR.GH.E...RVFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAML
Retrocopy LVSWNSILAAYARNGHVEGVERVFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAML

Parental  GAYALNEDSSLARKTFAQMPGKNEVSWDAMLTACTQAGDSVSIFDKMPQKDVFAWTSMLLAYARNGHLVN
          GAYALNED...A...F..MP....VS.......C..A..S..IFD.MPQ.....WT.ML...A.N.....
Retrocopy GAYALNEDVDSAQRIFREMPEIDLVSCNTVMRCCRDARQSKLIFDSMPQRALSSWTTMLAVLAKNSPGEE

Parental  AQKTFDEMPQHSLLSWSAILSVHAHSWDLKYAERIISGMPEYDLVSRNSILAAYARNGHVEGAKRVFDSM
          ....F..M....L...S..........DL..........P..DL.S.NS.L.AYA..GH.....R.F..M
Retrocopy TKSFFYQMLELDLT--SCMIMFLSQPSDLELVKATFDQIPQRDLCSWNSVLSAYAQ*GHCDFGLRLFNKM

Parental  EARDLVSWTTIL
          ...D.VSW.T.L
Retrocopy PEMDMVSWNTML

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_20 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Selaginella moellendorffii	SELMODRAFT_20534	6 retrocopies	retro_smoe_18, retro_smoe_19, retro_smoe_20 , retro_smoe_21, retro_smoe_28, retro_smoe_29,