RetrogeneDB ID: retro_xmac_4

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556730.1:1112621..1113512(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000020124
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: lrrc30
• Ensembl ID: ENSXMAG00000002735
• Aliases: None
• Description: leucine rich repeat containing 30 [Source:ZFIN;Acc:ZDB-GENE-050506-25]

Sequence

>retro_xmac_4
ATGGGTGGGAAGCAGTCACGCAGCCTGTCCAACTCAGAGTTGAATGAGGTGAGTGTGGGCCAAAGGAGGAAGGGTACAAT
TAGAGACGAGCAGCCCAGCCTGTCCTGGGCAGCGGAGAGGATCCGTAAACAAACCAGCGTCCACTTTGGTTTCAGTACTC
TGAGTTTAGCCATGCGGGGGTTGGATGAAACCCCCGCTGAGCTGTGGGAGCTCCAGGACCTTCAGAAACTCAACTTGTCC
ATGAACTGTCTGTGCTCCTTGCCTCCCGCTCTGGGCTCTCTGGATAATCTGGTGATTCTCAACTTATTGGGAAACAGCCT
GTCCAGCCTCCCCCCTGAGATCGGCCTGCTGAAGAAGCTTCGCGTGCTGTTCGCCTGTCGCAACCGCCTGAGTGAAGTCC
CTGAGGAGCTGGGCTCCTGCACATGCCTGGAGGTGCTGAGCTTGGCCAACAACCAGATCTCCAGCCTCCCCAGCAGCTTG
GCTGCCATGCATCATCTGACCAAACTCAACCTCAGTCACAACCGCATTGTTCACATCCCCACCTGTGTCTACAGCATGAA
AGGACTGGTCTTCCTGCACTTGGCCTGCAACCGCTTGGAGACCATAGCAGATCAGATTCAGGACCTGGTTAACTTGAAGA
TCCTGATCGTGGAGGGAAACAGCATACACACTCTTCCAAAGACTTTGTGTTTCTTGGATTCATTAGAGCTTCTGAATGTG
GACTTTAACGAGCTGCAAAGTGTGCCTGATGAGATGTACCAGCTGAGCAGACTCAGGCGGTTAGCCTGCCACCCACTGGA
TAAAGGACTTCATATAATTCACAACCCGCTCCTCAAGCCTATCCATGAGGTGCTGCAAGGTGGACTCAGTGCCCTGTATA
ACTACCTCAAG

Alignment

ORF - retro_xmac_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 97.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQRGVSHDRDQKNQLDTGSKTTSAMAQEEDSLS-SADKIQR-FSKQSGHNVLSLARRGLKDAPGELWELQ
          G....S......N....G.........E..SLS..A..I....S...G...LSLA.RGL...P.ELWELQ
Retrocopy GKQSRSLSNSELNEVSVGQRRKGTIRDEQPSLSWAAERIRKQTSVHFGFSTLSLAMRGLDETPAELWELQ

Parental  ELEKLNLSLNNLKALPPQLGLLSNLLVLNLWGNQLSSLPAEIGQLRRLRVLFVYRNRLTEVPEELGACTQ
          .L.KLNLS.N.L..LPP.LG.L.NL..LNL.GN.LSSLP.EIG.L..LRVLF..RNRL.EVPEELG.CT.
Retrocopy DLQKLNLSMNCLCSLPPALGSLDNLVILNLLGNSLSSLPPEIGLLKKLRVLFACRNRLSEVPEELGSCTC

Parental  LEVLSLANNQLSSLPASLSNLTRLRKLNLSHNLMAHLPGCIYSMKALVFLDLSCNRLENVAENIQALLEL
          LEVLSLANNQ.SSLP.SL.....L.KLNLSHN...H.P.C.YSMK.LVFL.L.CNRLE..A..IQ.L..L
Retrocopy LEVLSLANNQISSLPSSLAAMHHLTKLNLSHNRIVHIPTCVYSMKGLVFLHLACNRLETIADQIQDLVNL

Parental  KILIMEGNQLQSLPRGLCFLIRLELLNLDFNHIRDLPEEMHHLSRLQKLACHPLDKGLHIVHNPLMKPLK
          KILI.EGN....LP..LCFL..LELLN.DFN.....P.EM..LSRL..LACHPLDKGLHI.HNPL.KP..
Retrocopy KILIVEGNSIHTLPKTLCFLDSLELLNVDFNELQSVPDEMYQLSRLRRLACHPLDKGLHIIHNPLLKPIH

Parental  EVMEGGLAALFNYLR
          EV..GGL.AL.NYL.
Retrocopy EVLQGGLSALYNYLK

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_4 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_4 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
Oreochromis niloticus	ENSONIG00000009892	1 retrocopy	retro_onil_3,
Tetraodon nigroviridis	ENSTNIG00000005041	1 retrocopy	retro_tnig_8,
Takifugu rubripes	ENSTRUG00000002387	1 retrocopy	retro_trub_22,
Xiphophorus maculatus	ENSXMAG00000002735	1 retrocopy	retro_xmac_4 ,