RetrogeneDB ID: retro_xtro_8

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173146.1:377050..380668(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000015632
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: dse
• Ensembl ID: ENSXETG00000032776
• Aliases: None
• Description: dermatan sulfate epimerase precursor [Source:RefSeq peptide;Acc:NP_001120268]

Sequence

>retro_xtro_8
ATGGCTCTAAATTATACAGAACACTATATTTTTCTGTTTATTACTATTTTGTTCTTCTTTTTCATTGATAAATCTGCTAG
CAATTCATCCGATTGGTTGTTGCTGACTAATAATGTTGCTCAGTATCACAAATTATATGAATTTACATCTAGTGCCAAAC
AGAAGAGTGGTTTACATCCAAATTTGTACTTTGATGCTACAAATGTTCAAGAATTAAGGCAGAAATCACATACTAGTCAC
ATACATTTATATAGGACAATTAGAAATGCTGTAATGAAGATGCTCTCTAATCCATCATACTATTTGCCTCCACCAAAGCA
TGCTGATTTTACAGCAAAATGGAATGAAATTTATGGAAACAACCTTCCTCCTCTGGCACTGTATTGCCTGCTTTCTCCAG
ATGATAAAACCGCATTTACTTTTGTACTTGAGTATATGGACAGGATGGCTAATTACAAAGACTGGTTAGTCCAAACTGCT
CCTGGTGATGAAGTGCCTCTTGGGCATTCATTAACTGGCTTTGCCACAGCCTATGACTTTCTGTATAGTTCACTCGATAA
TGATAGAAGGCAACGATATATTAAAAAGATCCAAATGGCCAGTGAAGAAATGTATGAATATTCTAAAATTCGCTCATGGG
GAAAACAGTTTCTTCACAACCACCAAGCTACTAATATGCTAGCACTGCTTACAGGAGCATTGGTTGTACAGGTTTATAGA
GAAGCCCAGGCTAATGTTTGGAAACAAACTGTGGTTGATGTAATGGAAAAGACCATGTTTCTTCTAAATCATGTTGTTGA
TGGCTCTTTGGATGAAGGAGTTGCTTATGGAAGTTATACTTCTAAATCTATTACTCAGTATGTTTTCTTAGCACATCGAC
ATTTTGGTATCAATCACTTTGAGAACACCTGGTTGAAAATGCACTTCTACTTTTATTATTCTACCCTGCTGCCAGGTTTT
CAGAGAACAATTGGAATAGGAGACTCAAACTATAACTGGTTTTATGGTCCTGAAAGCCAGTTGGTGTTTCTGGACACATT
TATTTTAAAGAATGGGATAGGGAATTGGCTAGCCTATCAGATCCGAAAACACAGACCTAAAGATGGACCTATGGTACCAT
CTACAGCACAGAGGTGGAGCACCCTTCATACAGAATATCTATGGTACAATGCAGATCTTTCTTTGCATCCTCCTCCTGAT
CATGGCACTGCAAAAATGCACTTGTTTCCAAACTGGGGAGTTGTGACTTATGGAGCTGGATTACCAAATACTCAGACTAA
TACATTTTTCTCTTTCAAATCTGGAAAGCTTGGTGGTCGGGCAGTTTATGATATTGTTCATTTTCAACCATACTCTTGGG
TAGATGGATGGAGAAGTTTCAATCCAGGGCATGAGCATCCTGATCAAAACTCCTTTACATTTGCTCCCAATGGACAAGTC
TTTGTCTCTGAAGCACTATATGGACCAAAAATGAGTTATTTAAATAATATACTAGTTTTTGCTCCATCACCTACGAGTCA
GTGTAATAAACCTTGGGAAGGACAGTTGGGAGAATGCTCACAGTGGCTTAAATGGACAACCGAAGAATCTGGTGATGTAT
CTGGTGAGATTATAACAGCCAATCAGCATGAAGAAATGGTATTTGTAAGTGGTGAAGCAGTCTCTGCTTATTCGTCTTCC
ATGAGATTAAAGAGTGTTTACCGTGGTTTACTGCTTTTAAACCATCAGACTCTTTTGGTAATTGATCATATAGAGAAGTA
TCAAGATTCTCCAATATCTCTAGCTAGTGCCTTCTTCCACAATCTGGATATTGATTTTAAATATGTTGCTTTTAAATTTT
TAAACAAATACAATGGCGCTATGATGGATATTTGGGATGCTCACTACAAAATGTTTTGGTTAGACCAAAATGGTAATAGC
CCCTCTGCAAGGATACAAGAAGCAGAACAGGCAGCTGAATTTAAGAAGCGTTGGACGCAATTTGTAAATGTAACCTTTCA
ATTGAATGACAAAATTTCAAGAATCGCATACTTATTCTTTGGGCCATATGTTAATGTATCAGATCTAAAGTTTCTAGATG
ATAGTAAATTCGGGGTTAAGATTTCTGTAAAGATTAACAATACTGAAAATATTGTATCTTTAGTTACTGAATATAATGAT
TTAGAGGCCCGATTTAGCTTTCTTGGATTTGGCGGGTTTGCAAAAGTAGAGAATCAAGAAAAAATAGTACGGTTTGGCTT
AGGGGTTGATCATATTAGAAAACATGAACCTGTTGGTTTAAATATATTTCATTTTGGCTTGAAAGTAAATGTAATGATTG
GATTGATATTGTGCATAGGTCTGGTCATTTTAGCATTTAACTGGAGATTCTATATTTCCTTTAGTAAGCTGATGCGCTGG
ATCCTAGTATTGATTATTACACTTTATTTTTTTGAATTACTAGATGTATGGAGTACATGTACCCAACCCATTTGTGCTAA
GTGGAACAGTGAAATAGCAGACAGTGAAAATAAATATGAAAGGCAATCTATAAATCTCCCAGCTATAATTATCACCTCTC
TTCCCAGTTCAGGAGCTGAGATTTTAAAGCAACTTTTTTTCAACAGCTCTGATTTCATATATATTAGAGTCCCTACCGCT
TATATTGATATTCCAGATGGAGAGTTTAAGGTTGATTCGTTTGTCGATGCATGTGAATGGAGTAGTTCTGATGTTCAGGA
AGGACATTTTAAATTAATCCAAGGTTGGCTGCAGTCACTACTTCAGAATACAAAAATTCATTTACAAAACATTGATTTGC
ATGAGCCTAGCAAACCAAAACTTTTTCATCACAGTATCATCACTAAAGATAAAAAAAGAAGATTTAAAAGAAGGGACCCA
TTTCCAGAACAAAAAAATAGAATCAAAGGTAGCTATGACAGAGATGCAGAGTACATTAGACACCTTAGGAAACAATTAAT
AAAGTTTCCAAATGCTCAGCCTGTACTTGGTTTAAGCAGTGGAAGCTGGACATTAAAATTACCTTTTATTCAAAATATTA
TTGGACCTTCGTTGAGAGCAATATTTGTTGTTCGAGACCCTCGTTCATGGATTTATACATTGCTATATAAAAGCAGGCCT
AATCTATTCTCTTTGAGGAATATCCCTCAGCGTTTATATGAAATATTCAAAGAAGAAGAAAAACAGAAATGTAAGTCTAA
TGCAGGCTACGCATTTGAATATGAATCATTAGAAGATGAACTCTTTGATTCAGAATCAAATCCTCTTTCAAAACTGTCCC
ACTTGTGGTTATCAAACACAGCTGCAGCACGGAGGATAAACAGAAACTTGCCTGCAATAAATTATCTCTTGGTTAAATTT
GAAGACATTATAAACTCGCCACAAGAAACAGCAGAACAGATCTATACATTTTTTGGAATTCCTATTTCTCCTGCAAGTTT
AAACCAAATACTTTTTGCTAGTTCCACAAACTTATTTTATCTTCCACAAGAAGGAGAGATATCCCCATCAAGCTTAAATA
CTTGGAAACTTAATATGCCTAAGGAAGATATTAAATTAATTGAGAATATATGTTTAACACAAATGCAACAGCTTGGATAT
ACAAAGTATATAGATTAA

Alignment

ORF - retro_xtro_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.19 %
• Parental protein coverage: 65.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMLYFSKGEMETLRAQAASSHQHISARINEAVHVMLTNPSEYLPPWDPKEFSARWNEIYGNNLGALAMY
          .P.LYF.......LR.....SH.H....I..AV..ML.NPS.YLPP.....F.A.WNEIYGNNL..LA.Y
Retrocopy HPNLYFDATNVQELRQKSHTSHIHLYRTIRNAVMKMLSNPSYYLPPPKHADFTAKWNEIYGNNLPPLALY

Parental  CVLNPDNTEALGLAREYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFLYNSFSKQQKVRFLEVIA
          C.L.PD...A.....EYM.RMA....WLV..AP.DEVPL.HSL.GFATAYDFLY.S.......R....I.
Retrocopy CLLSPDDKTAFTFVLEYMDRMANYKDWLVQTAPGDEVPLGHSLTGFATAYDFLYSSLDNDRRQRYIKKIQ

Parental  NASVNMYETSFRRGWGFQYIHNHQPTNCVALLTGSLVMMNQGYLQEAYFWTKQVLTIMEKSIVLLNDVTD
          .AS..MYE.S..R.WG.Q..HNHQ.TN..ALLTG.LV.......Q.A..W...V...MEK...LLN.V.D
Retrocopy MASEEMYEYSKIRSWGKQFLHNHQATNMLALLTGALVVQVYREAQ-ANVWKQTVVDVMEKTMFLLNHVVD

Parental  GSLYEGVAYGSYTTRSLFQYMFLVQRHFDINHFGHPWLKEHFAFMYRTVLPGFQRTVAIADSNYNWFYGP
          GSL.EGVAYGSYT..S..QY.FL..RHF.INHF...WLK.HF.F.Y.T.LPGFQRT..I.DSNYNWFYGP
Retrocopy GSLDEGVAYGSYTSKSITQYVFLAHRHFGINHFENTWLKMHFYFYYSTLLPGFQRTIGIGDSNYNWFYGP

Parental  ESQLVFLDKYVLRNGSGNWLAEQIHANRVQEGPGTPAKGQRWCTLHTEFLWYDATLQSTPPPDFGTPQLH
          ESQLVFLD...L.NG.GNWLA.QI...R...GP..P...QRW.TLHTE.LWY.A.L...PPPD.GT...H
Retrocopy ESQLVFLDTFILKNGIGNWLAYQIRKHRPKDGPMVPSTAQRWSTLHTEYLWYNADLSLHPPPDHGTAKMH

Parental  YFEDWGVVTYGSSLPAEINRPFLSFKSGKLGGRAIFDIVHKNKYKDWIKGWRNFNAGHEHPDQNSFTFAP
          .F..WGVVTYG..LP......F.SFKSGKLGGRA..DIVH...Y..W..GWR.FN.GHEHPDQNSFTFAP
Retrocopy LFPNWGVVTYGAGLPNTQTNTFFSFKSGKLGGRAVYDIVHFQPY-SWVDGWRSFNPGHEHPDQNSFTFAP

Parental  NGFPFITEALYGPKYTFLNNALMFSPSVSESCFAPWQGQVTEDCTSKWLKYKQGEAADSQGRVVAAVEKS
          NG..F..EALYGPK...LNN.L.F.PS....C..PW.GQ..E...S.WLK....E..D..G....A....
Retrocopy NGQVFVSEALYGPKMSYLNNILVFAPSPTSQCNKPWEGQLGE--CSQWLKWTTEESGDVSGEIITANQHE

Parental  GVVFIRGEGVGAYSPNLKLKSVQRNLILLHPQLLLLVDHIHLDRGSTLEATSSFFHNVDMPFEATS---I
          ..VF..GE.V.AYS....LKSV.R.L.LL..Q.LL..DHI.....S.....S.FFHN.D..F........
Retrocopy EMVFVSGEAVSAYSSSMRLKSVYRGLLLLNHQTLLVIDHIEKYQDSPISLASAFFHNLDIDFKYVAFKFL

Parental  DSVHGAIIRHRDGMYKMYWMDDTGQSEKAVIASTSYPQGYPYNGTNYVNVTTYLRKPITRAIYVFIGPSV
          ....GA.....D..YKM.W.D..G.S..A.I.............T..VNVT..L...I.R..Y.F.GP.V
Retrocopy NKYNGAMMDIWDAHYKMFWLDQNGNSPSARIQEAEQAAEFKKRWTQFVNVTFQLNDKISRIAYLFFGPYV

Parental  DVESFSVHGD
          .V.......D
Retrocopy NVSDLKFLDD

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	4.64 RPM	3.74 RPM
SRP007412_heart	6.84 RPM	6.84 RPM
SRP007412_kidney	6.84 RPM	6.84 RPM
SRP007412_liver	1.39 RPM	8.68 RPM
SRP007412_skeletal_muscle	0.68 RPM	2.28 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_8 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_8 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8 ,