RetrogeneDB ID: retro_xtro_14

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173214.1:129309..130995(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000030128
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: XB-GENE-5895314
• Ensembl ID: ENSXETG00000007381
• Aliases: None
• Description: hypothetical protein LOC100136946 [Source:Jamboree;Acc:XB-GENE-5895314]

Sequence

>retro_xtro_14
CTGATTTCAGCGATGGCGGCTGCTGATCTGAGAGACGAGCTGAGCTGCTCCATCTGCCTGAGCATTTATACTGATCCGGT
ATCCCTGCCCTGTGGCCATAACTTCTGCCGGGGCTGCATTGGGGGGGTGCTGGGTATCCAAGAGGGGTCTGGGCGTTATT
CCTGCCCTGAATGCAGAGCTGAGTATCAGGAGTACCCTGCCCTGCCCAGGAACAGAGCTCTGGGGAACATAGCAGAGAGG
TTCCGTCCGACTGAGACAGAGCCGGGGGAGACTGGGATCTTCTGCACTTACTGTCTCCTCTCTCCTGTACCTGCTGCTAA
ATCCTGTCTCCTGTGTGAGGCTTCTCTGTGTGATACCCACCTGAGGGGGCACTGCCAGTCAGCAGAACATGTACTCACTG
AGCCCACCGCTTCCTTTATGGGGAGAAAATGTTCTGTACACAATGAGCCCCTAAAGTATTTCTGCTGGAAGGACTCTGCC
TGTATCTGTGTGTCCTGCTGCCTGGCCGGGGAGCACCGGGGCCACAGGGTGGAGCTGCTGAGTGAGGCCTCTGAGAAGAA
GAAAGAGAAACTGAGGAAAGTTCTGGAGAAACTGAGCCCAGAGAGAGAGGAGACTGAGAGAGGAGCCCAGAGGCTGCAGG
AGCGCAGGAGAGAAGTGGCAGAAGCGGCAGCCGGTGAGACAGAGAGAGTCACTGCCCTGTTTAGGGGCATCAGGGAACAG
CTGGAAGCCCTAGAGAAGCGACTCCTGAGTGACATCTCCAGGCAGAAAGAGGAACTTTGCCTCCAACTCACTGAGCTGAT
CCAACAGCTGGAAATAAAGAAGGATGAGCTGTCCAGGAAGATCCGGCACATTGAGGAGCTGTGCAACATGGCAGATCCAC
TCACTGTCCTACAGGAACAATGGGAATCCCATGGAGCTGCCTTTTGTGGGGCTGAGGGGGCAGATACTGAGGGCAGAGAG
AGAGAGGGTACTGAGGGGGCAGATACTGAGGGCAGAGAGAGAGAGGATACTGAGGGGGCAGATACTGAGGGCAGAGAGAG
AGAGGGTATAAAGGTCCCGGCTGTAGGGGATCTGGATGTGGGTCGGATCTCAGAGACATTACTCACAGGCTTAGCTGGGA
TTGTGACTGGGGTAAAGGGAAGAGTGATCCCTGGGCAGGAGGCTACAGAGCTGGTACTGGATATAAACACGGCTGGGAAT
GGTGTATCTGTATCAGGGGACGGGAAATCTGCTTCCTACTCACTTACAGGCCAGCGTCGCCCACAAACCCCAGAGAGATT
TCAGGTTTATGCTCAGGCTTTAAGCACCAGGAGTTTCCCCTCAGGGCGACATTACTGGGAAGTGGAGGGCAGTGAATCAG
GGAGCTGGAGGGTAGGGGCGGCCTATCCCAGTATAGAGAGGGGAGGGGGTCAGTCCTACATTGGGAATAATAACAAGTCC
TGGGGTTTAATCAGATGGAATAATAACTATACAGTGATACATGACAATAAAGTCACACAGTTACCCCACGCCCCTTCCTG
CAGGAGAATCAGGATCTCATTGGACTATGAGGCTGGACGGCTGTCCTTTTATGAGCTGAGTGAGCCAATCAGGCACTTAC
ACACCTTCACTGCCTCCTTCACTGAGCCCCTTCATGCTGCATTCTGGGTAGGGTGGGATGGTGCCTGGGTGAGAATCAAT
AGTTAG

Alignment

ORF - retro_xtro_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YTDPVSLPCGHNFCRGCIGGVLGTQEGSGRYSCPECRGRAEYQERPALPRNRALGNIAERFRPTETEPGE
          YTDPVSLPCGHNFCRGCIGGVLG.QEGSGRYSCPECR..AEYQE.PALPRNRALGNIAERFRPTETEPGE
Retrocopy YTDPVSLPCGHNFCRGCIGGVLGIQEGSGRYSCPECR--AEYQEYPALPRNRALGNIAERFRPTETEPGE

Parental  TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPTTSFMGRKCSVHHKVLEYHCCEGSA
          TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPT.SFMGRKCSVH...L.Y.C...SA
Retrocopy TGIFCTYCLLSPVPAAKSCLLCEASLCDTHLRGHCQSAEHVLTEPTASFMGRKCSVHNEPLKYFCWKDSA

Parental  CICVFCCLAGGHRGHRVELLSKASEKKKKKLRKVLEKLSPEREETERGAQRLQERRGELEEKAAIETERV
          CICV.CCLAG.HRGHRVELLS.ASEKKK.KLRKVLEKLSPEREETERGAQRLQERR.E..E.AA.ETERV
Retrocopy CICVSCCLAGEHRGHRVELLSEASEKKKEKLRKVLEKLSPEREETERGAQRLQERRREVAEAAAGETERV

Parental  TALFRGIREELEALEKRLLSDISRQKEELSLTLTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ
          TALFRGIRE.LEALEKRLLSDISRQKEEL.L.LTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ
Retrocopy TALFRGIREQLEALEKRLLSDISRQKEELCLQLTELIQQLEIKKDELSRKIRHIEELCNMADPLTVLQEQ

Parental  WESHGAAFCGAKGADNEGRESEDTEGADND-TKGADNEG---RGRE--DIKVPAVGDLDVGRISETLLTG
          WESHGAAFCGA.GAD.EGRE.E.TEGAD.......D.EG....GRE...IKVPAVGDLDVGRISETLLTG
Retrocopy WESHGAAFCGAEGADTEGREREGTEGADTEGREREDTEGADTEGREREGIKVPAVGDLDVGRISETLLTG

Parental  LAGIVTGVKGRIY-GQEATELVLDINTAGNRVSVSGDGKSASYSRTDQRRPQTPERFQV-SQALSTRSFP
          LAGIVTGVKGR...GQEATELVLDINTAGN.VSVSGDGKSASYS.T.QRRPQTPERFQV..QALSTRSFP
Retrocopy LAGIVTGVKGRVIPGQEATELVLDINTAGNGVSVSGDGKSASYSLTGQRRPQTPERFQVYAQALSTRSFP

Parental  SGRHYWEVEGSESGGWRVGAAYPSIERVGYQSLIGNNNKSWCLYRGNNNYTVVHDWEVTQLPHVPSCRRI
          SGRHYWEVEGSESG.WRVGAAYPSIER.G.QS.IGNNNKSW.L.R.NNNYTV.HD..VTQLPH.PSCRRI
Retrocopy SGRHYWEVEGSESGSWRVGAAYPSIERGGGQSYIGNNNKSWGLIRWNNNYTVIHDNKVTQLPHAPSCRRI

Parental  RISLDYEAGRLSFYELSEPIRHLHTFTVSLTEPLHAAFCV-VGGACVRIIS
          RISLDYEAGRLSFYELSEPIRHLHTFT.S.TEPLHAAF.V...GA.VRI.S
Retrocopy RISLDYEAGRLSFYELSEPIRHLHTFTASFTEPLHAAFWVGWDGAWVRINS

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	2.63 RPM	0.21 RPM
SRP007412_heart	1.33 RPM	0.13 RPM
SRP007412_kidney	1.33 RPM	0.13 RPM
SRP007412_liver	2.93 RPM	1.41 RPM
SRP007412_skeletal_muscle	0.62 RPM	0.06 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_14 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_14 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018057	1 retrocopy	retro_cjac_418,
Xenopus tropicalis	ENSXETG00000007381	1 retrocopy	retro_xtro_14 ,