RetrogeneDB ID: retro_xtro_10

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180905.1:10429..11581(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000031141
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: acadl
• Ensembl ID: ENSXETG00000001085
• Aliases: None
• Description: acyl-CoA dehydrogenase, long chain [Source:Jamboree;Acc:XB-GENE-958719]

Sequence

>retro_xtro_10
GCCACACCCATGCAAGACCTGAGCCAACGCACCGTCTACCGCGAAGACCACGAACAATTCCGCACGCAGGTACGCCGCTT
CTTCGAGCGCGAAATCGTGCCCTTCCACGCCCAGTGGGAACGCGACGGCATCGTGCCCAAGGAAGTGTGGCGCAAGGCCG
GACGCGAGGGCCTGCTCAACACCATGCTGCCCGAGCCCTACGGCGGCGGTGGCGACTTCGGCCACGCGGCGGTGCTGATC
GAGGAAGTGGCACGCACGGGCGCCAGCGGCCTGGGTTTTCCGCTGCACTCCGACATCGTCGCGCCCTACATCCACGCCTA
CGGCAGCACGGCGCAGAAAGACCGCTGGCTACCGCACATGGCCGCAGGCGCGCTGATCGGCGCCATCGCCATGACCGAGC
CCGGCGCGGGCAGCGACCTGAAATCGGTACGCACCACGGCACGGCGCGAAGGCGACCACTACGTCATCAACGGCGCCAAG
ACCTTCATCACCAACGGCATCAACGCCGGACTCGTCATCGTCGTGTGCAAGACCGCACCCGAGCTGGGCGCCAAAGGCGT
GTCGCTGATCGTGGTGGAGGAGGGCACACCGGGCTTCAGCAAAGGCCGCAAACTCGAAAAAATCGGCCTCATGGCGCAAG
ACACCTCCGAACTGTTCTTCGACCACGCCAAAGTACCCGCAGGGCATCTGCTGGGCGAGGAGAACCAGGGCTTCAAGTAC
CTGATGAAGGAACTCGCGCAAGAGCGTCTGGTGGTTGCAGTGCGCGCTGCCGCCTCCATCGAAGCCATGCTGCACCAAAC
CGTGGCCTACACACGCGAGCGCCGCGCCTTCGGCCAAACGGTGTTCGAATTCCAGAACACGCGCTTCAAGCTCGCCGAAG
CCAAGGCCCAGGCCACCATGCTGCGCGTGTTCGTAGACGACTGCATCGCCCTGCACCTGCGCCGCGCCCTCACACCCGAA
CGCGCCGCCATGGTCAAACTCAACGCCACAGCGTTGCAAAACCGCCTGCTCGACGAATTCCTGCAACTGCACGGCGGCTA
CGGCTACATGACCGAATACCAAGTGGGCCGCGCCTGGACCGATGCACGCATAGGCCGCATCTACGGCGGCAGCGACGAGA
TCATGAAAGAAATCATCGCCCGCACGCTGTAA

Alignment

ORF - retro_xtro_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.52 %
• Parental protein coverage: 86.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKSLMDIGTRRIFSSDHDIFRESARKFFQQEVVPYHAEWEKAGQVSRNLWEKAGQQGLLGTSTPEEHGGI
          A....D...R.....DH..FR...R.FF..E.VP.HA.WE..G.V....W.KAG..GLL.T..PE..GG.
Retrocopy ATPMQDLSQRTVYREDHEQFRTQVRRFFEREIVPFHAQWERDGIVPKEVWRKAGREGLLNTMLPEPYGG-

Parental  GGDILSSAIVWEEQMYVNCTGPGFSLHSDIVMPYISRYGSKSQVEKYIPQMTAGKCIGAIAMTEPGAGSD
          GGD....A...EE.......G.GF.LHSDIV.PYI..YGS..Q.....P.M.AG..IGAIAMTEPGAGSD
Retrocopy GGDFGHAAVLIEEVARTGASGLGFPLHSDIVAPYIHAYGSTAQKDRWLPHMAAGALIGAIAMTEPGAGSD

Parental  LQGVRTNAKKDGSDWILNGSKVFITNGWMSDVVIVVAVTNREARTPAHGISLFLVDNGTKGFVKGRKLEK
          L..VRT.A...G.....NG.K.FITNG.....VIVV..T..E....A.G.SL..V..GT.GF.KGRKLEK
Retrocopy LKSVRTTARREGDHYVINGAKTFITNGINAGLVIVVCKTAPELG--AKGVSLIVVEEGTPGFSKGRKLEK

Parental  IGLKAQDTAELFFEDVRLPADALLGQENKGFYYLMAELPQERLLIADMALASCEFMFEETRNYVKQRKAF
          IGL.AQDT.ELFF.....PA..LLG.EN.GF.YLM.EL.QERL..A..A.AS.E.M...T..Y...R.AF
Retrocopy IGLMAQDTSELFFDHAKVPAGHLLGEENQGFKYLMKELAQERLVVAVRAAASIEAMLHQTVAYTRERRAF

Parental  GKTIAHLQTVQHKLAELKTQICIGRTFLDNCLQLHAEKRLDSATASMAKYWASDLQNSVATQCVQLHGGW
          G.T....Q....KLAE.K.Q....R.F.D.C..LH....L....A.M.K..A..LQN.......QLHGG.
Retrocopy GQTVFEFQNTRFKLAEAKAQATMLRVFVDDCIALHLRRALTPERAAMVKLNATALQNRLLDEFLQLHGGY

Parental  GYMWEYPIAKAYVDSRVQPIYGGTNEIMKELIARDI
          GYM.EY....A..D.R...IYGG..EIMKE.IAR..
Retrocopy GYMTEYQVGRAWTDARIGRIYGGSDEIMKEIIARTL

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	15.85 RPM
SRP007412_heart	0.00 RPM	307.24 RPM
SRP007412_kidney	0.00 RPM	307.24 RPM
SRP007412_liver	0.00 RPM	101.13 RPM
SRP007412_skeletal_muscle	0.00 RPM	314.83 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_10 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_10 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000487	1 retrocopy	retro_etel_761,
Xenopus tropicalis	ENSXETG00000001085	1 retrocopy	retro_xtro_10 ,
Xenopus tropicalis	ENSXETG00000007932	1 retrocopy	retro_xtro_42,
Xenopus tropicalis	ENSXETG00000016078	1 retrocopy	retro_xtro_43,