RetrogeneDB ID: retro_xmac_18

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556724.1:46616..47729(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019448
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSTR5 (2 of 2)
• Ensembl ID: ENSXMAG00000012731
• Aliases: None
• Description: somatostatin receptor 5 [Source:HGNC Symbol;Acc:11334]

Sequence

>retro_xmac_18
ATGGAGCCCTGGATGTTCCCATCATCCCCACCAAACCTAACGGAGCACCTTTTGTATGACAGCTTCATGCAGGGGAATGA
GTCCAGCATTAATGGAAGCTACATAGACCACAGCTTCAACCAAACCAGCACTGTGGTCATCACATGTATGTACTTTCTAG
TTTGCGCTGTGGGACTTTGTGGGAACGCTTTGGTCATCTACGTTATCCTGCGCTATGCCAAGATGAAGACAGTCACCAAC
ATCTATATTCTCAATCTGGCGGTAGCAGATGTGCTCTTTATGCTCGGACTGCCATTCATTGCCATCCAGCTGGCACTAGT
TCACTGGCCCTTTGGGCCTGTGCTCTGCAGGGTCGTTATGACTGTGGACTCCCTGAACCAGTTCACGTCCATCTTCTGCC
TTATGGTAATGAGCATTGACCGCTACTTGGCAGTGGTGCATCCCATAAAGTCCACAAAGTGGCGAAAACCACGCATCGCT
AAAACTATTAACTTAGCCGTATGGGTAGTTTCACTGTTAGTCAATCTGCCCATCGTTATCTACACTGGTGTGATTACAAA
GCACAATGGCTGCTTCTGCACCATTGTGTGGCCAGAACCTCAAGAAACCTACTACACAGTCTTCATGTTCTACACCTTCA
TTCTGGGCTTCTTCCTTCCCCTAATGGTCATCTGCCTCTGCTACCTGCTCATCATCATCAAGGTAAAGTCTTCAGGCATC
CGAGTAGGCTCCTCCAAAAGGAAGCGATCAGAACGCAAGGTCACCCGGATGGTTTCCATTGTTGTGGCTGTGTTTGTGTT
CTGCTGGCTGCCTTTCTACGTTTTCAACGTCACCTCGGTGACAGGCAGCATCAGCACCACCCCCATCCTGAGGAGCACCT
TTGCCTTCGTGGTGGTTCTAGGATACGCCAACAGCTGTGCCAACCCAATCCTCTACGCCTTCTTATCAGAGAACTTCAAG
AAGAGCTTCCAGAATGTTCTCTGTCTTAAGAAGGTAGGAGGGCTGGATGAGGTTGATCGCAGTGACAGTCGGCAGGACAA
ATCTCGCATGATGAATGACCCAACAGAGACCCAGAGTACTTTGCTCAATGGTGACCTGCAGACCAGCATCTAG

Alignment

ORF - retro_xmac_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.87 %
• Parental protein coverage: 81.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQGSSTPVTAIIYFTVFLVGLTGNTLAIYVVLRYAKMKTVTNIYILNLAVADELYIIGLPFLTTQNVLSY
          F...ST.V....YF.V..VGL.GN.L.IYV.LRYAKMKTVTNIYILNLAVAD.L...GLPF...Q..L..
Retrocopy FNQTSTVVITCMYFLVCAVGLCGNALVIYVILRYAKMKTVTNIYILNLAVADVLFMLGLPFIAIQLALVH

Parental  WPFGSFLCRVVMTADSMNQFTSIFCLTVMSMDRYLAVVHPIRSTKWRHPRVAKVVSAAVWAVSFIVVLPV
          WPFG..LCRVVMT.DS.NQFTSIFCL.VMS.DRYLAVVHPI.STKWR.PR.AK....AVW.VS..V.LP.
Retrocopy WPFGPVLCRVVMTVDSLNQFTSIFCLMVMSIDRYLAVVHPIKSTKWRKPRIAKTINLAVWVVSLLVNLPI

Parental  VIFSDVQDMFNS--CNMNWPEPKDVWSTAFIIYTATVGFFGPLLVICLCYLLIVIKVKSSGARVGFINRR
          VI...V....N...C...WPEP.....T.F..YT...GFF.PL.VICLCYLLI.IKVKSSG.RVG...R.
Retrocopy VIYTGVITKHNGCFCTIVWPEPQETYYTVFMFYTFILGFFLPLMVICLCYLLIIIKVKSSGIRVGSSKRK

Parental  RSERKVTRMVVVIVVVFVLCWLPFYIINMVNLVVIIPESSVTAGIYFFAVVLSYANSCANPLLYGFLSDN
          RSERKVTRMV...V.VFV.CWLPFY..N.......I...........F.VVL.YANSCANP.LY.FLS.N
Retrocopy RSERKVTRMVSIVVAVFVFCWLPFYVFNVTSVTGSISTTPILRSTFAFVVVLGYANSCANPILYAFLSEN

Parental  FKQSFRKVLCVKGMRCAANGVDDGDPSVPRTEKT
          FK.SF..VLC.K.......G.D..D.S..R..K.
Retrocopy FKKSFQNVLCLK----KVGGLDEVDRSDSRQDKS

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_18 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_18 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000018944	2 retrocopies	retro_gacu_1, retro_gacu_11,
Gadus morhua	ENSGMOG00000018538	1 retrocopy	retro_gmor_13,
Oreochromis niloticus	ENSONIG00000017693	1 retrocopy	retro_onil_17,
Tetraodon nigroviridis	ENSTNIG00000014076	1 retrocopy	retro_tnig_9,
Xiphophorus maculatus	ENSXMAG00000012731	1 retrocopy	retro_xmac_18 ,