RetrogeneDB ID: retro_smoe_19

Retrocopy location

• Organism: Spikemoss (Selaginella moellendorffii)
• Coordinates: GL377603:545149..545805(+)
• 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_19
CTCGTGTCTTGGAATTCCATTCTAACGGCATACGCCCGGAAAGGGCATGAACGGGAAAAATGTGTTTTCGATTCAATGGA
GGCTCGTGACCTTGTGTCATGGACGACAATCTTGGTTGCCTTGTCGCAGGGCGGAGATTTGCACGGAGCAAAGCTTTTGT
TTGATGCAATGCCGCAGCACGATCTCGTCGCCTGGACCGCGATGCTTGGCGCGTACGCACTGAACGAGGATGTCGATTCG
ACACAGAGGATTTTCCGCGAGATGCCTGAGATAGATCTCGTTTCGTGCAACACCGTGATGCGATGCTGCGTGATGCTAGA
CAATCAAAGCTTATATTTGACTCCATGCCGCAGAGAGCTCTCTCGTCATGGACAACAATGCTCGCTGTTCTTGCCAAGAA
CAGCCCCGGGGAGGAAACCAAGAGCTTTTTCTATCAAATGCCGGAGCTTGATCTTACTTCCTGTACGATAATGCTGCTCT
GACAACCCTCAGACTTGGATCTTGTGAAGGCCACCTTTGATCAAATGCCGCAGCGAGACCTGTGCTCTTGGAACTCTGTT
CTGTCGGTGTATGCCCAATCAGGGCATTGTGACTTTGCTTTAAGTCTCTTTAACGAGATGCCCGAAATGGATATGGTTTC
GTGGAACAATATGTTA

Alignment

ORF - retro_smoe_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVSWNSILTAYARKGHEREKRVFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAMLG
          LVSWNSILTAYARKGHEREK.VFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAMLG
Retrocopy LVSWNSILTAYARKGHEREKCVFDSMEARDLVSWTTILVALSQGGDLHGAKLLFDAMPQHDLVAWTAMLG

Parental  AYALNEDSSLARKTFAQMPGKNEVSWDAMLTACT-QAGDSVSIFDKMPQKDVFAWTSMLLAYARNGHLVN
          AYALNED.......F..MP....VS.......C...A..S..IFD.MPQ.....WT.ML...A.N.....
Retrocopy AYALNEDVDSTQRIFREMPEIDLVSCNTVMRCCV<DARQSKLIFDSMPQRALSSWTTMLAVLAKNSPGEE

Parental  AQKTFDEMPQHSLLSWSAILSVHAHSWDLKYAERIISGMPEYDLVSRNSILAAYARNGHVEGAKRVFDSM
          ....F..MP...L.S....L.......DL.........MP..DL.S.NS.L..YA..GH...A...F..M
Retrocopy TKSFFYQMPELDLTSCTIMLL*QPSDLDL--VKATFDQMPQRDLCSWNSVLSVYAQSGHCDFALSLFNEM

Parental  EARDLVSWTTIL
          ...D.VSW...L
Retrocopy PEMDMVSWNNML

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_19 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,