RetrogeneDB ID: retro_xtro_39

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174735.1:1413..2046(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: hsd17b10
• Ensembl ID: ENSXETG00000007721
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:Jamboree;Acc:XB-GENE-986902]

Sequence

>retro_xtro_39
AAAGGTCAGGCGGTCGCCCGGGAGATTGGCGGCGCCTGCGTGCAATGCGACGTCAGCAGCGAAGCGGATGGCCAGACCGT
AGTCGCCAAGGCCACCTCGCTGGGCAAGCTCATGGGCCTGGTCAACTGCGCCGGCATCGCTTCTGCAGAGAAAACGGTCG
GCAAGAACGGCGCGCATGCCCTGGCACTCTTCCAGAAAACCATCAGCGTCAACCTCATCGGCACCTTCAACATGATCAGG
CTGGCCGCCGAGGCCATGGTCAAAAACGATCCCGAGCCCACAGGCGAGCGCGGCGCACTGATCTCGACCGCCAGCGTGGC
GGCCTATGACGGCCAGATAGGCCAAGCGGCTTACAGCGCCTCGAAAGGCGGCGTGGTCGGCATGACCCTGCCCATCGCAC
GCGATCTGGCGCGCCACGGTATCCGCAACATGACGATTGCCCCCGGCATCTTTGGCACCCCCATGCTGTTCGGCATGCCA
CAGCAAGTACAGGATGCGCTCGCCGCAGGCGTTCCCTTCCCAAGCCGCCTGGGCAAGCCCGAGGATTACGCCAAACTGGT
GCAGCACATCCTGGAAAACGACATGCTCAACGGCGAAGTCATCCGCCTCGATGGCGCCATCCGCCTGGCGCCG

Alignment

ORF - retro_xtro_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.72 %
• Parental protein coverage: 82.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGKTVAESLGEKCAFSPTDVTSEADVKNALELARTKFGRVDVVVNCAGIAVAAKTYNLNKQLPHSLEDFQ
          .G..VA...G..C.....DV.SEAD.......A.T..G.....VNCAGIA.A.KT....K...H.L..FQ
Retrocopy KGQAVAREIGGACV--QCDVSSEADGQTVVAKA-TSLGKLMGLVNCAGIASAEKT--VGKNGAHALALFQ

Parental  RVINVNIAGTFNVIRLAAGEMGKNDPDEDGHRGVIVNTASVAAFDGQVGQAAYSASKGGIVGMTLPIARD
          ..I.VN..GTFN.IRLAA..M.KNDP...G.RG....TASVAA.DGQ.GQAAYSASKGG.VGMTLPIARD
Retrocopy KTISVNLIGTFNMIRLAAEAMVKNDPEPTGERGALISTASVAAYDGQIGQAAYSASKGGVVGMTLPIARD

Parental  LAPMGIRVVTIAPGLFATPLLVGLPEKVRNFLAKQVPFPSRLGDPGEYAHLVQSIVENPMLNGEVIRLDG
          LA..GIR..TIAPG.F.TP.L.G.P..V...LA..VPFPSRLG.P..YA.LVQ.I.EN.MLNGEVIRLDG
Retrocopy LARHGIRNMTIAPGIFGTPMLFGMPQQVQDALAAGVPFPSRLGKPEDYAKLVQHILENDMLNGEVIRLDG

Parental  ALRMQP
          A.R..P
Retrocopy AIRLAP

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	50.20 RPM
SRP007412_heart	0.00 RPM	114.57 RPM
SRP007412_kidney	0.00 RPM	114.57 RPM
SRP007412_liver	0.00 RPM	56.08 RPM
SRP007412_skeletal_muscle	0.00 RPM	31.07 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_39 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_39 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39 ,
Xenopus tropicalis	ENSXETG00000021320	2 retrocopies	retro_xtro_35, retro_xtro_37,