RetrogeneDB ID: retro_xmac_19

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556736.1:1650068..1651187(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019812
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: B3GNT3 (2 of 2)
• Ensembl ID: ENSXMAG00000018521
• Aliases: None
• Description: UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 [Source:HGNC Symbol;Acc:13528]

Sequence

>retro_xmac_19
AGAGCTTCAAAGATGAGAAAAAAATTCAGAATTTTCTTCTTTGTTGGAGCCCTTGGCCTGCTGGCTTTCCCTTTCTTTAT
GTACTCTGATCATCAGAAAACTTTCCAGAAGAACACTGCTGAGAACAACAGACAAAAAAAGACACCCATCAAAAACATCT
CTTACATACACTCTTGGGAAAAATGCCAGCAAAATCTGACTGCAGCCAACATCACAGGCTTCTCAAATCTTCCTCAGAAT
ATCAAAGACTTTCTCTTCTATTGTCACTGTCGACATTTCCCCATGCTGCTGGATCTCCCTGATAAATGTGGAGGAGCTGA
GAAATCGGGAGACGTTTTCCTTCTGCTGGTCATCAAGAGCTCCCCGGCCAACTACGAACGGCGGGAGGTGCTGCGGAAAA
CATGGGGTAAAGAGAGGTTATACAACGGCATGTCGATTCGAAGGATCTTCATTTCCGGAGTTTCAGGTGACAGTTATGAA
AAAGAAAGACTGAACAATCTCCTGAAACTGGAGCAACAGGAGCACAGAGATGTTCTCCAGTGGGACTTCAGTGACACTTT
TTACAACCTCACTTTGAAGCAAATACTGTTCCTGGAATGGATGGAAAGAAACTGTCCGAATGCTCGCTTCCTCCTGAATG
GGGACGACGATGTGTTTGCCCACACAGACAACATGGTTGTGTATCTGCAAAGCCTCAAGGAAAATAATGGGAGCAGGCAT
CTCTTCACTGGTCATCTGATCCAGAATGTGGGGCCCATCAGAGCAGCAGGGAGCAAATATTTTATCCCAGTTCAAGTTCA
GAAATCAGACACATACCCTCCGTATTGTGGCGGAGGGGGCTTCCTTCTGTCAGGATACACAGCAATGCTTATATACCGCA
TGTCCAAATCCATACCAGTTCTTCCCATCGATGATGTTTACATGGGGATGTGTCTGGCCAAAGCCGGACTTGGCCCGTCC
TCACACATGGGTGTGAAGACAGCGGGGCTGCACATTCCCTCCAAAAAAGTAGACAATTTCAGTCCGTGCTTCTATAAAGA
CGTTTTGCTGGTGCACAGATTCCTCCCAGCTCAGATGTACCTGATGTGGCACAGCACACAGAACCCAAAACTAAAATGT

Alignment

ORF - retro_xmac_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 96.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RHFPMLLDIPNKCGGTNASSDVFLLLVIKSSAVNYDRREVLRKTWAKERLSNGVWIRRIFISGTMGTGHE
          RHFPMLLD.P.KCGG...S.DVFLLLVIKSS..NY.RREVLRKTW.KERL.NG..IRRIFISG..G...E
Retrocopy RHFPMLLDLPDKCGGAEKSGDVFLLLVIKSSPANYERREVLRKTWGKERLYNGMSIRRIFISGVSGDSYE

Parental  TKRLNQLLKLEQSKYNDIIQWDFKDTFYNLTLKQMLFLEWMERNCPRANFLFNGDDDVFANTDNMVLYLQ
          ..RLN.LLKLEQ....D..QWDF.DTFYNLTLKQ.LFLEWMERNCP.A.FL.NGDDDVFA.TDNMV.YLQ
Retrocopy KERLNNLLKLEQQEHRDVLQWDFSDTFYNLTLKQILFLEWMERNCPNARFLLNGDDDVFAHTDNMVVYLQ

Parental  NFERKGGRKHLFAGHLIYNVGPIRSPQSKYYVPEQLYESKLYPAYCGGGGFLLSGYTASVIYANSHSIPI
          ......G..HLF.GHLI.NVGPIR...SKY..P.Q...S..YP.YCGGGGFLLSGYTA..IY..S.SIP.
Retrocopy SLKENNGSRHLFTGHLIQNVGPIRAAGSKYFIPVQVQKSDTYPPYCGGGGFLLSGYTAMLIYRMSKSIPV

Parental  LPIDDVYMGMCLAQAGLKPEHHLGIAVQMLIINPLFNKKISRLIVSFTREISYIHQ
          LPIDDVYMGMCLA.AGL.P..H.G.....L.I.....KK.......F.......H.
Retrocopy LPIDDVYMGMCLAKAGLGPSSHMGVKTAGLHIP---SKKVDNFSPCFYKDVLLVHR

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_19 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_19 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xiphophorus maculatus	ENSXMAG00000003895	1 retrocopy	retro_xmac_15,
Xiphophorus maculatus	ENSXMAG00000018521	1 retrocopy	retro_xmac_19 ,