RetrogeneDB ID: retro_xmac_12

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH557059.1:177826..178930(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000020394
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: npy8ar
• Ensembl ID: ENSXMAG00000000370
• Aliases: None
• Description: neuropeptide Y receptor Y8a [Source:ZFIN;Acc:ZDB-GENE-990415-175]

Sequence

>retro_xmac_12
ATGGAGCTGCAGCACAACACCAATCACAACCAGGCCTTGTGGAGAGAGATACCATGGGAGTCCACGGAGGACTGCTCGCT
CTCAGTGAGCGGGACCACTTTCCTCATCATCGCTTACAGCATAGTGATGGCCGTGGGGCTCATCGGGAACGCCTGCTTGG
TTTTTGTCATCATGCGGCACAAGGAGATGCAAAACGTTACCAACATCTTCATTGTCAACCTGTCTTGTTCTGATATTCTT
ATGTGCATTATATGCCTCCCAGTCACCATAATTTACACACTGATGGACCAGTGGATCCTCGGTGACACAATGTGCAAGCT
CACGCCCTTCATCCAGTGCATTTCAGTTACTGTCTCCATCTTCTCCCTCGTCCTCATTGCCTTGGAGCGCTACCAGCTCA
TCGTCCACCCGACTGGATGGAAACCACTGGTGAGCCAGTCCCACGTGGCAGTGGCCGTCACCTGGATCGTGGCCTGCCTG
ATATCTGTGCCTTTCCTAAAGTACAGTGTACTTACCTTGCCTTTCCAGAACCTGAGCCTCCCCATCCCTGTCAGCGACCA
CCTCATTTGCATGGAAGTGTGGCCGTCCATTCCAAAGCGCCGCGCATACACCACCTCCCTGCTTGTCTTCCAATACCTGC
TTCCTCTCACCCTCATCTTGGTCTGCTACCTGCACATCTACCTGCGTCTGAGAAGGAGGAAGGACATGGTGGAGCGCGGC
AGGAATGCGACTCAAAAGAAGAACAAGGGCTCCACAAGGATCAACGCCATGCTGATCTCCATTGTTGTGGCCTTCGCTCT
CTCCTGGCTTCCACTCAACATCTTCAACACGGTGTTTGACTGGAACCACGAGGCCATCCCATCTTGTGGCCATGACGTCA
TCTTTTCTTTCTGCCACCTCACAGCGATGGTCTCCACTTGCGTCAACCCGATCATCTATGGGTTCCTCAATAGCAACTTC
CAGAAGCAGCTTAAGTCCACTGTATTGCGCTGTCGCTGTTGGGGGCCGGTGGATAGGTACGAAATCGTTCCACTGTCTAC
TGTTAGCACAGAGGTCACCAAAGGGTCAGTCTTCAGCAATGGATCAATCACTATCAACTCATAA

Alignment

ORF - retro_xmac_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 92.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLDTSQCPPSVGGATFLIVAYSAVIAIGLLGNAGLVFIITRQQELRNVTNILIANLSCSDILMCVVCLPV
          W..T..C..SV.G.TFLI.AYS.V.A.GL.GNA.LVF.I.R..E..NVTNI.I.NLSCSDILMC..CLPV
Retrocopy WESTEDCSLSVSGTTFLIIAYSIVMAVGLIGNACLVFVIMRHKEMQNVTNIFIVNLSCSDILMCIICLPV

Parental  TVIYTLMDHWVLGEALCKVTPFVQCMSVTVSIFSLVLIALERHQLILHPTGWTPAAGHSYLAVGLTWLVG
          T.IYTLMD.W.LG...CK.TPF.QC.SVTVSIFSLVLIALER.QLI.HPTGW.P....S..AV..TW.V.
Retrocopy TIIYTLMDQWILGDTMCKLTPFIQCISVTVSIFSLVLIALERYQLIVHPTGWKPLVSQSHVAVAVTWIVA

Parental  CFISLPFLSFNILTNDPFQNISLPSNPFRDHLICMELWPSDKHRLAYTTSLLIFQYCLPLLLVLLCYLRI
          C.IS.PFL....LT..PFQN.SLP..P..DHLICME.WPS...R.AYTTSLL.FQY.LPL.L.L.CYL.I
Retrocopy CLISVPFLKYSVLTL-PFQNLSLPI-PVSDHLICMEVWPSIPKRRAYTTSLLVFQYLLPLTLILVCYLHI

Parental  FIRLRRRRDMLERSRR-TRGAQRINVMLLAIVIAFALC----WLPLNVFNTLFDWHHQALPKCQHDAVFS
          ..RLRRR.DM.ER.R..T...........A..I.........WLPLN.FNT.FDW.H.A.P.C.HD..FS
Retrocopy YLRLRRRKDMVERGRNATQKKNKGSTRINAMLISIVVAFALSWLPLNIFNTVFDWNHEAIPSCGHDVIFS

Parental  ACHLTAMASTCINPVVYGFLNSNFQRELRTTLQRCQCGTRAGESYESFPLSTVGSEGITKATSLNRMGSV
          .CHLTAM.STC.NP..YGFLNSNFQ..L..T..RC.C.......YE..PLSTV..E..TK.......GS.
Retrocopy FCHLTAMVSTCVNPIIYGFLNSNFQKQLKSTVLRCRCWGPV-DRYEIVPLSTVSTE-VTKGSVFSN-GSI

Parental  CVPS
          ...S
Retrocopy TINS

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_12 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_12 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Tetraodon nigroviridis	ENSTNIG00000013601	1 retrocopy	retro_tnig_10,
Takifugu rubripes	ENSTRUG00000018631	1 retrocopy	retro_trub_17,
Xiphophorus maculatus	ENSXMAG00000000370	1 retrocopy	retro_xmac_12 ,
Xiphophorus maculatus	ENSXMAG00000008242	1 retrocopy	retro_xmac_16,