RetrogeneDB ID: retro_smoe_4

Retrocopy location

• Organism: Spikemoss (Selaginella moellendorffii)
• Coordinates: GL377569:3124003..3124486(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: SELMODRAFT_28066
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: SELMODRAFT_159225
• Aliases: None
• Description: None

Sequence

>retro_smoe_4
ATCGCGGTCGGGGAGAGGATTCCCGATGGAGAGCTCTCCTACTTCGACGAGAGCGGCGCCATCCAGAGCATCAAGGTGTC
GGACCTGACGAGCAAGAAGAAGGTGGTGATCTTCGCGGTGCCCGGAGCTTTCACGCCCACTTGCTCCTCCAAGCACGTCC
CGGGATTCATCGACAAGGCGGACGAGCTCAAGTCCAAGGGGGTGGACACCATCGCCTGCGTCTCCGTGAACGATGCCTTC
GTCATGAAGTCGTGGGGCGAGGCGCTGGGCGTCAATGGCAAGATCCTCATGCTGTCCGACGGCAATGGCAAGTTTACCCG
CGATCTGGGAGTGACCGTGGATCTTTCAGACAAGGTGGAGGGATTGGGAGTGAGGTCCCGGCGCTACTCTCTGCTGGCCG
AGGATGGGATCGTCAAGGTGTTGAATCTCGAGGAGGGTGGTGCCTACACGGTGAGCAGCGCCGACGAGATCCTCAAGGCA
CTC

Alignment

ORF - retro_smoe_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.42 %
• Parental protein coverage: 97.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGVEEIIPDGTLSYFDKDGKLQNVSIYALAEKKKVVLFGVPGAFTPTCSLKHVPGYIDKAPELKAKGVDK
          I.V.E.IPDG.LSYFD..G..Q......L..KKKVV.F.VPGAFTPTCS.KHVPG.IDKA.ELK.KGVD.
Retrocopy IAVGERIPDGELSYFDESGAIQSIKVSDLTSKKKVVIFAVPGAFTPTCSSKHVPGFIDKADELKSKGVDT

Parental  ILCLTVNDPFVVREWAKTYPEDSAVMFLADGSATYTKSLGLELDLTER--GMGIRSKRFALLLDDLVVKA
          I.C..VND.FV...W............L.DG....T..LG...DL.....G.G.RS.R..LL..D..VK.
Retrocopy IACVSVNDAFVMKSWGEALGVNGKILMLSDGNGKFTRDLGVTVDLSDKVEGLGVRSRRYSLLAEDGIVKV

Parental  ANIEEGGDFKVSSADDILAVL
          .N.EEGG...VSSAD.IL..L
Retrocopy LNLEEGGAYTVSSADEILKAL

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_4 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4 ,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,