RetrogeneDB ID: retro_xmac_17

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH559498.1:7491..8349(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000020299
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: tpst1l
• Ensembl ID: ENSXMAG00000007886
• Aliases: None
• Description: tyrosylprotein sulfotransferase 1, like [Source:ZFIN;Acc:ZDB-GENE-040316-1]

Sequence

>retro_xmac_17
ATGATCGGCAAGCTGAAACAGAACCTGCTGGTGGCCTGCCTGGTCATCAGCTCAGTCACCGTCTTTTACCTTGGCTGGCA
TGCGATGGAATGTCACCATCGCTCTGAGGAGCGCAGCCATCCAGGAGGAGTCTTGCCTCTGTCCGCGCTGGGAGGCAGCA
TGCGGACCACCTTACGGACAGGCCAGAACCTCAGCACACCGTTTGTTTACAACAAAGACACGCCACTGATTTTTATAGGG
GGTGTGCCAAGAAGCGGTACCACACTGATGAGAGCAATGTTAGATGCCCACCCTGAGGTGCGCTGTGGAGAGGAGACGCG
CGTCATTCCCCGCATCCTGGCCATGAAACAGATGTGGAGCCGTTCAGGACGGGAGAAGATGCGCCTGGATGAGGCTGGTG
TAACAGATGAGGTGCTGGATGCTGCCATGCAGGCCTTCCTACTGGAAATCATTGTCAAACACGGTGAGCCGGCAAACTTC
CTCTGCAATAAGGACCCGTTTGCACTGAAGTCGCTCTCCTACCTGGCCAAGATTTTCCCACGTGCCAAGTTTGTGCTCAT
GATTCGTGATGGGAGGGCATCGGTTCACTCCATGATCTCACGGAAAGTAACCATTGCAGGATTTGACCTGGGCAGCTATC
GCGACTGCCTGACCAAGTGGAATCGGGCGATAGAAACTATGTACACTCAGTGCTTGGAGGCAGTGGACAAATGCCTACCT
ATGCACTATGAACAGTTGGTCCTCCATCCTGAGAAATGGATGCAGACACTGTTGAAGTTCCTAAAAGTTCCTTGGAATGA
TGCTGTCCTTCACCATGAGGAGCTTATTGGGAAAGCAGGGGGAGTTTCCCTTTCCAGG

Alignment

ORF - retro_xmac_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.69 %
• Parental protein coverage: 62.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPEDTPLIFIGGFPRSGTTLMRVMLDAHSAVRCGEETRVIPRLLAMRATWSRSVRERIRLDEAGVTDQVL
          ...DTPLIFIGG.PRSGTTLMR.MLDAH..VRCGEETRVIPR.LAM...WSRS.RE..RLDEAGVTD.VL
Retrocopy YNKDTPLIFIGGVPRSGTTLMRAMLDAHPEVRCGEETRVIPRILAMKQMWSRSGREKMRLDEAGVTDEVL

Parental  DAAVRAFLLEVIVGHGEPAARLCNKDPFALKSLSYLARIFPKAKFVLMLRDGRATVHSMISRKVTISGFD
          DAA..AFLLE.IV.HGEPA..LCNKDPFALKSLSYLA.IFP.AKFVLM.RDGRA.VHSMISRKVTI.GFD
Retrocopy DAAMQAFLLEIIVKHGEPANFLCNKDPFALKSLSYLAKIFPRAKFVLMIRDGRASVHSMISRKVTIAGFD

Parental  LSSYRDCLTKWSSAVEAMFSQCQAVGETRCLPVRYEQLVLHPEQQMRDLLHFLELKWDSSVLHHEELIGK
          L.SYRDCLTKW..A.E.M..QC.......CLP..YEQLVLHPE..M..LL.FL...W...VLHHEELIGK
Retrocopy LGSYRDCLTKWNRAIETMYTQCLEAVD-KCLPMHYEQLVLHPEKWMQTLLKFLKVPWNDAVLHHEELIGK

Parental  AGGVSLSR
          AGGVSLSR
Retrocopy AGGVSLSR

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_17 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_17 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
Callithrix jacchus	ENSCJAG00000004198	1 retrocopy	retro_cjac_2241,
Xiphophorus maculatus	ENSXMAG00000007886	1 retrocopy	retro_xmac_17 ,