RetrogeneDB ID: retro_xtro_57

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181459.1:2632..3739(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: adh5
• Ensembl ID: ENSXETG00000009304
• Aliases: None
• Description: alcohol dehydrogenase 5 (class III), chi polypeptide [Source:Jamboree;Acc:XB-GENE-977214]

Sequence

>retro_xtro_57
ATGAAATCCCGTGCCGCCGTCGCCTTCAAGGCCGCAGAACCGCTGCAAATCGTCGAACTCGATGTGGCGCCGCCGCAAAA
GGGCGAAGTACTGGTGCGCATCACCCACACCGGCGTATGCCATACCGACGCCTTCACCCTGAGCGGCGACGACCCCGAGG
GCCTGTTCCCCGCCGTACTGGGCCACGAAGGCGCGGGCATCGTCGTTGAAGTGGGCGAGGGCGTCACCAGCGTCCGGCCC
GGCGACCACGTCATCCCGCTCTACACCGCCGAGTGCGGCGCGTGCCTGTTCTGCCAATCGGGCAAAACCAACCTGTGCGT
GGCCGTACGCGCCACCCAAGGCAAGGGCGTGATGCCCGACGGCACCACACGCTTCTCGTACAACGGCCAGCCCGTGTACC
ACTACATGGGCTGCTCCACGTTCAGCGAATACACCGTAGTGGCCGAAGTGTCGCTGGCCAAGGTACACCCCGATGCCAAC
CCCGAGCAAGTCTGCCTGCTGGGCTGCGGCGTAACCACCGGCCTGGGCGCGGTGAAAAACACCGCCAAAGTGCAACCCGG
AGACACAGTGGCCGTATTCGGCCTGGGCGGCATCGGTCTGGCGGTAATCCAGGGCGCCAAGCTGGCCCAGGCCGGGCGCA
TCATCGCCATCGACACCAACCCAGGCAAATTCGACCTGGCGCGCACCTTCGGCGCCACCGACTGCGTGAACCCCAAGGAC
TACGACAAACCCATCCAACAGGTGATCGTAGAGATGACCGGCTGGGGCGTGGATCACTCCTTCGAGTGCATAGGCAACGT
CAACGTCATGCGTGCGGCGCTGGAGTGCGCGCACCGCGGCTGGGGCCAGAGCGTCATCATCGGCGTAGCGGGTGCGGGGC
AGGAAATCTCCACACGCCCGTTCCAGCTGGTAACGGGCCGCAAGTGGCTGGGCACGGCCTTTGGCGGCGTCAAAGGCCGC
TCGCAACTGCCTGGCATGGTGGAAGACGCCATGGCCGGCAGAATCCAGCTCGAACCCTTCGTAACCCACACCATGGGCCT
GCAGGACATCAACGCCGCATTCGACCTGATGCACGCAGGCAAGTCCATCCGCAGCGTGGTGCACTAC

Alignment

ORF - retro_xtro_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.96 %
• Parental protein coverage: 98.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKCKAAVAWEAGKPLSIEEVEVAPPKAHEVRIKIVSTAVCHTDAYTLSGADPEGCFPVILGHEGAGIVES
          .K..AAVA..A..PL.I.E..VAPP...EV...I..T.VCHTDA.TLSG.DPEG.FP..LGHEGAGIV..
Retrocopy MKSRAAVAFKAAEPLQIVELDVAPPQKGEVLVRITHTGVCHTDAFTLSGDDPEGLFPAVLGHEGAGIVVE

Parental  VGEGVTRVKPGDKVIPLYIPQCGECKFCLNPKTNLCQKIRITQGKGFMPDGSSRFTCKGQQIFHFMGTST
          VGEGVT.V.PGD.VIPLY...CG.C.FC...KTNLC...R.TQGKG.MPDG..RF...GQ...H.MG.ST
Retrocopy VGEGVTSVRPGDHVIPLYTAECGACLFCQSGKTNLCVAVRATQGKGVMPDGTTRFSYNGQPVYHYMGCST

Parental  FSEYTVVADISVAKIDDSAPLDKVCLLGCGISTGYGAVINTAKVEPGSTCAVFGLGGVGLAVIMGCKVAG
          FSEYTVVA..S.AK....A....VCLLGCG..TG.GAV.NTAKV.PG.T.AVFGLGG.GLAVI.G.K.A.
Retrocopy FSEYTVVAEVSLAKVHPDANPEQVCLLGCGVTTGLGAVKNTAKVQPGDTVAVFGLGGIGLAVIQGAKLAQ

Parental  ATRIIGIDLNKDKFVKATEFGATDCLNPADFKKPIQDVLIEMTDGGVDYSFECIGNVGVMRAALEACHKG
          A.RII.ID.N..KF..A..FGATDC.NP.D..KPIQ.V..EMT..GVD.SFECIGNV.VMRAALE..H.G
Retrocopy AGRIIAIDTNPGKFDLARTFGATDCVNPKDYDKPIQQVIVEMTGWGVDHSFECIGNVNVMRAALECAHRG

Parental  WGTSVIVGVAASGQEIATRPFQLVTGRVWKGTAFGGWKSVDSVPKLVSEYMAKKIKVDEFVTHTLPFNSI
          WG.SVI.GVA..GQEI.TRPFQLVTGR.W.GTAFGG.K.....P..V...MA..I....FVTHT.....I
Retrocopy WGQSVIIGVAGAGQEISTRPFQLVTGRKWLGTAFGGVKGRSQLPGMVEDAMAGRIQLEPFVTHTMGLQDI

Parental  NEAFELMHAGKSIRGVLNY
          N.AF.LMHAGKSIR.V..Y
Retrocopy NAAFDLMHAGKSIRSVVHY

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	21.05 RPM
SRP007412_heart	0.00 RPM	41.14 RPM
SRP007412_kidney	0.00 RPM	41.14 RPM
SRP007412_liver	0.07 RPM	21.13 RPM
SRP007412_skeletal_muscle	0.00 RPM	20.53 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_57 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_57 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57 ,