RetrogeneDB ID: retro_xmac_27

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH558872.1:3173..3580(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXMAG00000013667
• Aliases: None
• Description: None

Sequence

>retro_xmac_27
CTGCTCTGTGTTGTTTTCTCTCCTTCAGATCAGAACAACGTGAAAATCAAAGCTGAACCTGGAGATGACCGCATTCTGCC
ATGTAAAGATCCTGACCAGGAGCAGATTAAAGCCGTAGAGTGGAGCAGAACTGACCTGGAGTCAGGATTTGTCCTCCTGT
ACAGAGATTCACGTTTTGATCTAACAAACCAGGATCCATCTTACAGGAACCGGGTTGATCTGCTGGTTGGTCAGATACAG
AAAGGAGACGCGTCTTTGATTCTGCAGAACACAACAACTGATGACAGCGGAACGTATGAATGTCACGTTGTTAAATCAGC
TGAGAGGAAACTGATCAGCTCCGTCAGCCTGGTTGTAGCTCCTCCTCCAGGTGAGTGTTTGTCTCTGGATCAGAACCAGC
AGCTTCC

Alignment

ORF - retro_xmac_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 80.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLSVVFWQFLSAAAQNYVTIKATVGENVILPCEDPDQEEIIVVEWSRTDLGPESVLLYRDSQFDPINQDP
          LL.VVF....S...QN.V.IKA..G...ILPC.DPDQE.I..VEWSRTDL....VLLYRDS.FD..NQDP
Retrocopy LLCVVF----SPSDQNNVKIKAEPGDDRILPCKDPDQEQIKAVEWSRTDLESGFVLLYRDSRFDLTNQDP

Parental  SYRNRVDLLVRQIKKGDASLILQNTTTDDSGTYECYVVKTTEMKLICSVSLVVAPPPPPGIP-SSSPPPA
          SYRNRVDLLV.QI.KGDASLILQNTTTDDSGTYEC.VVK..E.KLI.SVSLVVAPPP......S.S.P.A
Retrocopy SYRNRVDLLVGQIQKGDASLILQNTTTDDSGTYECHVVKSAERKLISSVSLVVAPPPGECLS<SGSEPAA

Parental  S
          S
Retrocopy S

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_27 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_27 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Xiphophorus maculatus	ENSXMAG00000013667	1 retrocopy	retro_xmac_27 ,