RetrogeneDB ID: retro_xtro_47

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180656.1:20806..21757(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: agmat
• Ensembl ID: ENSXETG00000025999
• Aliases: None
• Description: agmatine ureohydrolase (agmatinase) [Source:Jamboree;Acc:XB-GENE-997016]

Sequence

>retro_xtro_47
ACGCAAACCGCAAAACCATCCCTGAACCAACCCCTGGGCGGCAACACCATGCCGCGCTTTGCCGGACTGGCCAGCATGAT
GCGTCTGCCCATGGCCACCTCGGCCCAGGGACTGGACGCCGCCTTCATCGGTGTACCCCTGGACATTGGAACCTCCAACC
GCTCGGGCACCCGCTTCGGGCCGCGCCAGATACGCGCCGAATCCAGCCTGCTGCGTCCCTACAACATGGCCACTGGCGCC
GCCCCCTTCGACGCCCTGCAAGTGGCCGACCTGGGCGATGTGCCCATCAACACCTATTCGCTGCCCAAATCGGTGGAGTG
CATCACCGCCTTCTACGACCAGGTTCTGTGCCACGGCTGCGTGCCCCTGACCCTGGGCGGCGACCACACCATTGCCCTGC
CCATCCTGCGCGCCATGGCCCGCCGCCATGGGCCGCTGGCCCTGATCCACGTCGATGCCCACGCCGACATCAACGACGAC
ATGTTCGGTGAAAAGATCGCGCACGGCACCCCTTTTCGCCGCGCCGTTGAGGAAGGTCTGCTCAGCGGCGACAAGGTCTG
GCAGATCGGTCTGCGCGGCAGCGGCTATGCGGCCGACGATTTTGACTGGCCGCGCCGACAAGGCTTCACCATAGTTGCGG
CGCACGAAGTCTGGTACCAGTCACTGGCCCCCCTGATGGCCCAGGTGCGCGAACGCATCGGGCCGCACCATCCGGTGTAC
ATCAGCTTCGACATCGACGGCCTGGATCCCAGCTTCGCCGCTGGCACCGGCACCCCTGAAATCGGGGGCCTGAGCGTGCC
CCAGGGCCTGGAGATCGTGCGCGGCTGCCGAGGCCTGAACGTGGTGGGCGGCGATCTGGTCGAAGTCAGCCCGCCCTACG
ACACCAGCGGCAACACCGCCCTGCTGGGCGCCAATCTGCTGTACGAAATGCTGTGCATCCTGCCCGGGGTG

Alignment

ORF - retro_xtro_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.15 %
• Parental protein coverage: 92.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRRASGKFNVPPSAQYVARPAGVCTMMRLPYQETAQGLDAAFIGVPLDTGTSNRPGARFGPRHIRGESCM
          ...A....N.P.......R.AG...MMRLP....AQGLDAAFIGVPLD.GTSNR.G.RFGPR.IR.ES..
Retrocopy TQTAKPSLNQPLGGNTMPRFAGLASMMRLPMATSAQGLDAAFIGVPLDIGTSNRSGTRFGPRQIRAESSL

Parental  VRRYNISTRAAPFESLMVADIGDVNVNLYDLKDSCRRIRETYQKIMAAGCIPLTLGGDHTITYPILQAVA
          .R.YN..T.AAPF..L.VAD.GDV..N.Y.L..S...I...Y......GC.PLTLGGDHTI..PIL.A.A
Retrocopy LRPYNMATGAAPFDALQVADLGDVPINTYSLPKSVECITAFYDQVLCHGCVPLTLGGDHTIALPILRAMA

Parental  EKHGPVGLVHVDAHTDTGDTALGEKIYHGTPFRRCVDEGLLDCKRVVQIGIRGSSYSADPYGFCREQGFR
          ..HGP..L.HVDAH.D..D...GEKI.HGTPFRR.V.EGLL....V.QIG.RGS.Y.AD.....R.QGF.
Retrocopy RRHGPLALIHVDAHADINDDMFGEKIAHGTPFRRAVEEGLLSGDKVWQIGLRGSGYAADDFDWPRRQGFT

Parental  VVLAEDCWFRSLVPLMAEVRSQMGA-GPVYISFDIDGLDPSFAPGTGTPEIAGLTTSQGLEIIRGCRGLN
          .V.A...W..SL.PLMA.VR...G...PVYISFDIDGLDPSFA.GTGTPEI.GL...QGLEI.RGCRGLN
Retrocopy IVAAHEVWYQSLAPLMAQVRERIGPHHPVYISFDIDGLDPSFAAGTGTPEIGGLSVPQGLEIVRGCRGLN

Parental  VVGCDLVEVAPVYDQSGNTALTGANLLFEMLCVLPRV
          VVG.DLVEV.P.YD.SGNTAL.GANLL.EMLC.LP.V
Retrocopy VVGGDLVEVSPPYDTSGNTALLGANLLYEMLCILPGV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	2.56 RPM
SRP007412_heart	0.00 RPM	1.71 RPM
SRP007412_kidney	0.00 RPM	1.71 RPM
SRP007412_liver	0.00 RPM	25.97 RPM
SRP007412_skeletal_muscle	0.00 RPM	12.70 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_47 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_47 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000025999	2 retrocopies	retro_xtro_47 , retro_xtro_59,