RetrogeneDB ID: retro_xmac_24

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556751.1:1481796..1482960(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: kcnj8
• Ensembl ID: ENSXMAG00000017494
• Aliases: None
• Description: potassium inwardly-rectifying channel, subfamily J, member 8 [Source:ZFIN;Acc:ZDB-GENE-060308-1]

Sequence

>retro_xmac_24
ATGTTGTCCAGGAAGGGACTCATTCCTGAGGATTACTTGCTGACACGATTAGCTGAGGATGTTCTGCAGCCGAAGTTCAA
GGCCAAACAAGGGAAGGCTCGGTTTGTGGGGAAGAACGGCACCTGCAACGTTGCGCACACCAACATCCGAGAACAGGGTC
GGTTCTTACAGGACGTGTTCACCACACTAGTGGATTTGAAATGGCTCCACACTCTCATCATTTTCACCATGTCCTTCCTG
TGCAGCTGGCTCCTGTTCGGGATGATCTGGTGGCTTGTGGCTTTTGCGCACGGGGACCTGGGTGAAAAGGGGGATGATTT
TGTCCCGTGCGTAACCGACATCCACTCCTTCTCCTCCGCCTTCCTCTTCTCCATAGAAGTCCAGGTGACCATCGGCTTCG
GGGGTCGGATGATCACGGAGGAGTGCATCTCGGCCATCATCATCCTCATAGTGCAGAACATCGTGGGACTGGTCATCAAC
GCCATCATGCTGGGCTGCATCTTCATGAAAACTGCGCAGGCTCATCGGCGCGCGGAGACGCTCATCTTCAGCAAGCACGC
AGTCATCTCCCTCCGAAACAGCAAGCTGTGTTTTATGATCCGCATAGGAGACCTGAGGAAAAGCATGATCATCAGCGCCA
CCGTGCGGATGCAGGTGGTGAGGAGGAGCACCACGGAGGAGGGAGAGGTGGTGCCCCTTGACCAGATCGACATCCACATG
GATAATCCGGTGGGGACCAACGGGGTCTTCCTGGTGTCCCCCCTCATCATCTGCCATGTCATCGACAAGTCCAGCCCCTT
GTACGAGCTTTCACCGAACGACCTGCAGCACCAGGACCTGGAGGTGATCGTGGTGCTGGAGGGGGTGGTGGAGACCACCG
GCATCACCACGCAGGCCAGGACTTCCTACGTGTCGGAGGAGATCCTGTGGGGCCAGCGCTTCGTGCCGACGGTGTCCGAA
GACGACGGCATGTACGCAGTGGACTACTCCAAGTTTGGCAACACCGTCAAGGTACCGACGCCGTGCTGCAGCGCCAAGAA
GCTGGATGAGGCCGGTGGCATCGCACGGTTTAAGCTGAACGAGGGCGTCACCATGCGGCCGTCCGTGAGAAGGCGGAGGG
GGACCGCGATAGTGCGCAGGTCCAGAATGGAGAACAAGTGAGGC

Alignment

ORF - retro_xmac_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.81 %
• Parental protein coverage: 91.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLARKSIIPEEFGLPGLASRLPRKPVFRDRVNKARFIAKNGSCNLAHKNIREQGRFLQDVFTTLVDLKWR
          ML.RK..IPE...L..LA......P.F.....KARF..KNG.CN.AH.NIREQGRFLQDVFTTLVDLKW.
Retrocopy MLSRKGLIPEDYLLTRLAEDV-LQPKFKAKQGKARFVGKNGTCNVAHTNIREQGRFLQDVFTTLVDLKWL

Parental  FTLVIFTTTFVSSWLLFAMSWWLVAFAHGDMDPARKNETHCVTDVESFISAFLFSIEVQVTIGFGGRMIT
          .TL.IFT..F..SWLLF.M.WWLVAFAHGD..........CVTD..SF.SAFLFSIEVQVTIGFGGRMIT
Retrocopy HTLIIFTMSFLCSWLLFGMIWWLVAFAHGDLGEKGDDFVPCVTDIHSFSSAFLFSIEVQVTIGFGGRMIT

Parental  EHCLAAITVLILQNIVGLIINAVMLGCIFMKTAQSNRRAETLIFSRHAVIAVRNNRLCFMIRIGDLRKSM
          E.C..AI..LI.QNIVGL.INA.MLGCIFMKTAQ..RRAETLIFS.HAVI..RN..LCFMIRIGDLRKSM
Retrocopy EECISAIIILIVQNIVGLVINAIMLGCIFMKTAQAHRRAETLIFSKHAVISLRNSKLCFMIRIGDLRKSM

Parental  IIGATVRLQVVRKTTTPEGEIIPIHQIDVQTESAVASNSLFLLAPLIICHVIDKNSPLYDLSAMELQCSD
          II.ATVR.QVVR..TT.EGE..P..QID......V..N..FL..PLIICHVIDK.SPLY.LS...LQ..D
Retrocopy IISATVRMQVVRRSTTEEGEVVPLDQIDIHMDNPVGTNGVFLVSPLIICHVIDKSSPLYELSPNDLQHQD

Parental  LEVIVILEGVVETTGITTQARTSYVSEEIQWGHRFVPIVTEEEGVYSVDYSKFGNTVKVSTPSCSARELD
          LEVIV.LEGVVETTGITTQARTSYVSEEI.WG.RFVP.V.E..G.Y.VDYSKFGNTVKV.TP.CSA..LD
Retrocopy LEVIVVLEGVVETTGITTQARTSYVSEEILWGQRFVPTVSEDDGMYAVDYSKFGNTVKVPTPCCSAKKLD

Parental  EKPYILIQTLQKSELSHQNSLRKRNS--MRRNNSMRKGG
          E...I....L...........R.R.....RR.....K.G
Retrocopy EAGGIARFKLNEGVTMRPSVRRRRGTAIVRRSRMENK*G

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_24 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_24 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000001115	1 retrocopy	retro_gacu_7,
Tetraodon nigroviridis	ENSTNIG00000006480	1 retrocopy	retro_tnig_7,
Takifugu rubripes	ENSTRUG00000009953	1 retrocopy	retro_trub_1,
Xiphophorus maculatus	ENSXMAG00000017494	1 retrocopy	retro_xmac_24 ,