RetrogeneDB ID: retro_xmac_9

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH557076.1:114782..115853(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019566
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: aplnra
• Ensembl ID: ENSXMAG00000015247
• Aliases: None
• Description: apelin receptor a [Source:ZFIN;Acc:ZDB-GENE-060929-512]

Sequence

>retro_xmac_9
ATGGAATCCACTACGACTCCTTATGACTACTACGACTACGAGGAGACAGAGAACTCCACTATGTGCGACTATTCAGAGTG
GGCGCCATCGTACTCTGTCATCCCGGTGCTCTACATGCTCATCTTCATCCTTGGCCTCTCAGGGAATGGGATCGTCATCT
TTACCGTGTGGAGGGCTCAAGGCAAGCATCGAGCTGCTGACGTCTACATTGGCAACCTGGCATTAGCAGACCTCACCTTC
GTGGTCACTCTGCCCCTCTGGGCCGTTTATACCGCCATGGGCTACCACTGGCCCTTTGGAGTGGCTCTGTGCAAGATAAG
CAGCTACGTGGTGCTTCTCAACATGTACGCCAGTGTCTTCTGCCTCACCTGCATGAGCTTTGACCGGTATCTGGCCATCG
TCCACTCCCTGACCAGCTCCCAGCTGCTCACCCGTCGACACATTCGAGCCTCGCTCGCAGTCATCTGGGTGCTGTCTGGT
CTGCTGGCTGCCCCCACTCTTCTGTTTCGCACCACCAAGTACGATCAGCAAACCAACCGAACATCTTGTGCCATGGACTT
CAGTCTGGTCGTGACCATTAAGGAGCAGGAGAACCTGTGGATCGCTGGTCTCAGCATCTCCTCCTCAGCTCTTGGCTTTC
TCCTTCCCTTCCTGGCAATGATGGTGTGCTATTGCTTCATCGGCTGCACCGTCACCCGCCACTTCAACACCCTGCGTAAG
GAGGATCAGCGTAAAAGGAGACTGCTGAAGATCATCACCACCCTGGTGGTGGTGTTTGCTGTCTGTTGGCTGCCCTTCCA
CCTTGTGAAAACCGCTGATGCCTTGTCATACGTAGATTTGGTCCCTGCCACCTGCGACTTCCTGCGCTTCCTGCTGCTGG
CTCACCCCTACGCTACCTGCCTGGCCTACGTCAACAGCTGCCTCAACCCCTTCCTTTATGCCTTCTTTGACCTGCGCTTC
AGATCTCAGTGCCTGTGCCTCCTTAATCTGAAGAAATTCCTGCATGCCAGTCCAAACAGCTCCATGTCCTCGCAGAAGAC
AGAGGCTCAGTCACTGGCCACAAAGGTGTGA

Alignment

ORF - retro_xmac_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 96.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDFVVLPFNVLREIFAVFTLNFDRKLLFCHSLSSNKLRSRGTMLASLGAIWLLSGVLSLPTLLFRTTMQD
          S..VVL..N.....F......FDR.L...HSL.S..L..R....ASL..IW.LSG.L..PTLLFRTT..D
Retrocopy SSYVVL-LNMYASVFCLTCMSFDRYLAIVHSLTSSQLLTRRHIRASLAVIWVLSGLLAAPTLLFRTTKYD

Parental  LN-NQTICAMDFSLVTINQGHENLWIAGLSLSSSALGFLLPFLAMTIFYCFIGCTVTRHFNNLRKEDQKK
          ...N.T.CAMDFSLV......ENLWIAGLS.SSSALGFLLPFLAM...YCFIGCTVTRHFN.LRKEDQ.K
Retrocopy QQTNRTSCAMDFSLVVTIKEQENLWIAGLSISSSALGFLLPFLAMMVCYCFIGCTVTRHFNTLRKEDQRK

Parental  KRLLKIITTLVVVFAICWIPFHVLKSLDALSYLNLAPNSCGVVRFVLLAHPYATCLAYVNSCLNPFLYAF
          .RLLKIITTLVVVFA.CW.PFH..K..DALSY..L.P..C...RF.LLAHPYATCLAYVNSCLNPFLYAF
Retrocopy RRLLKIITTLVVVFAVCWLPFHLVKTADALSYVDLVPATCDFLRFLLLAHPYATCLAYVNSCLNPFLYAF

Parental  FDLRFRSQCLCLLNLKKAMHGQMSSMSSTLSAQTQKSEIQSLATKV
          FDLRFRSQCLCLLNLKK..H....S..S..S.Q..K.E.QSLATKV
Retrocopy FDLRFRSQCLCLLNLKKFLH---ASPNSSMSSQ--KTEAQSLATKV

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_9 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_9 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	ENSXMAG00000015247	1 retrocopy	retro_xmac_9 ,