RetrogeneDB ID: retro_xmac_25

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556810.1:1096602..1097117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: march5
• Ensembl ID: ENSXMAG00000007675
• Aliases: None
• Description: membrane-associated ring finger (C3HC4) 5 [Source:ZFIN;Acc:ZDB-GENE-070424-47]

Sequence

>retro_xmac_25
CCTGCAGGTGGCATCGAGTACTGCATCATTTACCCGAAGATGGGCCCGTTGGTGACCTCCTGCAGCAGGCGGACAGAGCC
AGCCCCTTCAACGCAGTCGGAGAGGTTGTTGGGACGCTGTACTGGTCAGCACTCACCTACGGAGCCGTGACCATCATGCA
GGTGGGGGGCATAAGAAGGATCTGTTTGTGATGGAGCGGGTTGACCCTATGTTCCTGCTCATGGACCTGCCGAACTTCCC
GGTACTGCTGGTCCTGGGGAAGATGATTTGCTGGGAGGATTACTTAGTCAGGCTGTGGTCTAGGCGCTCCTATAAACACA
GGGGTATCTACACAGCCTTCATCAGGTAGTGGCGGTTATCTGCCTCGTCTGTGTACCCACGGCCTCAGCACTGGTGACCA
CGTGTCTGTATCCAGAACTCTGTGTGGGGCGCTTATCTTTCCCTCCATAGCTAGTCTGGTGGGACGGCTGCTGTTCCGAC
TGGTTACCTCCAACCTGCAGTGCACCATACTGGGG

Alignment

ORF - retro_xmac_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.51 %
• Parental protein coverage: 62.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PQCNAEYLIVFPKLG-PIVYVLDLADRLISKAGPFAAAGIMVGSIYWTAVTYGAVTVMQVVG-HKEGLDV
          P....EY.I..PK.G.P....L..AD.....A.PF.A.G..VG..YW.A.TYGAVT.MQV.G.HK..L.V
Retrocopy PAGGIEYCIIYPKMG<PVGDLLQQAD----RASPFNAVGEVVGTLYWSALTYGAVTIMQVGG<HKKDLFV

Parental  MERADPLFLLIGLPTIPVMLILGKMIRWEDYVLRLWRKYSNKLQIFNSIF-PGIGCPVPRIPAEASPLAD
          MER.DP.FLL..LP..PV.L.LGKMI.WEDY..RLW...S.K.......F..G.G...PR.........D
Retrocopy MERVDPMFLLMDLPNFPVLLVLGKMICWEDYLVRLWSRRSYKHRGIYTAF>SGSGGYLPRLCTHGLSTGD

Parental  HVSATRILCGALVFPTIATIVGKLMFSSVNSNLQRTILG
          HVS..R.LCGAL.FP.IA..VG.L.F..V.SNLQ.TILG
Retrocopy HVSVSRTLCGALIFPSIASLVGRLLFRLVTSNLQCTILG

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_25 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_25 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020981	1 retrocopy	retro_btau_1749,
Macropus eugenii	ENSMEUG00000011031	1 retrocopy	retro_meug_1192,
Mus musculus	ENSMUSG00000023307	3 retrocopies	retro_mmus_1559, retro_mmus_3211, retro_mmus_3373,
Sarcophilus harrisii	ENSSHAG00000018432	1 retrocopy	retro_shar_459,
Xiphophorus maculatus	ENSXMAG00000007675	1 retrocopy	retro_xmac_25 ,