RetrogeneDB ID: retro_amel_371

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192409.1:776148..776824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSAMEG00000005036
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:HGNC Symbol;Acc:4800]

Sequence

>retro_amel_371
GGTCTGGCCATGGTAGAGCAGCTGGAGGGGCAAGGGGCCACTGCTTGCTTCTCGACCTGCCTAACTTCAATGGGGAGGCC
CAAGCCAAGCAGTTAGTGAAGAGGTGTGCCTTCGCCCCAGCTGACCTGACCTCAGAGAAGGACGTGCAAGCAGCCCTGAC
TTTAGCAAAAGAAAGATTTGGCCACGTGGATGTGTGGCAGTCAACTGTGCAGGCACTGAAGTGGCCATTAAGACATACGA
CTTCAAGAACAATCAGGTCCATACCTTGGAGGACTTCCAGCAAGTTCTTAATGTAATCTCACGGGTATCTTTAATGTGAT
CCACCTGGTGGCTGGTGAGAGGGGCCAGAATGAACCAGAGCAGGGAAGCCAACGTGGGGTCATCATCAACACTGCCAGCA
CTGGCTGCCTTTGAGGGCCAGGTTGGACAAGCTGCTTACTCTGCTTCCAAGGGGGGTCATAGTGGGCATGACACTGCCCA
CTGCTCCACCTCTAGCTCCCACGGGCATCCAAGTGAGAGCCACTGCTCCAGGCCTATTTGACACCCTGCTGCTGACCTGT
CTCCCAGAAGAGTGCGCAACTTGTAGGCCAGCCAGGTGTCCTTCCCCAGCTGAATGGGTGACCCTGCTGAGCATGGGCAT
CTGATTTAAGCCATCATCAAGAACCCATTCATCAGC

Alignment

ORF - retro_amel_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.71 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GLATAERLVGQGAAA-VLLDLPNSDGEVQAKKLGKSCAFAPADVTSEKDVQAALTLA-KEK-FGRVDVAV
          GLA..E.L.GQGA.A..LLDLPN..GE.QAK.L.K.CAFAPAD.TSEKDVQAALTLA.K.K...R..VAV
Retrocopy GLAMVEQLEGQGATA<LLLDLPNFNGEAQAKQLVKRCAFAPADLTSEKDVQAALTLA<KRKIWPRGCVAV

Parental  NCAGIAVAIKTYNLKKNQVHALEDFQRVLNV-NLLGTFNVIRLVAGEMGQNEPDQGGQRGVIINTAS-VA
          NCAG..VAIKTY..K.NQVH.LEDFQ.VLNV.NL.G.FNVI.LVAGE.GQNEP.QG.QRGVIINTAS..A
Retrocopy NCAGTEVAIKTYDFKNNQVHTLEDFQQVLNV<NLTGIFNVIHLVAGERGQNEPEQGSQRGVIINTAS>LA

Parental  AFEGQVGQAAYSASKGG-IVGMTLPIARDLAPVGIRVMTIAPGLFGTPLLTSLPE-KVRNFLASQVPFPS
          AFEGQVGQAAYSASKGG.IVGMTLP.A..LAP.GI.V...APGLF.T.LLT.LPE..VRN..ASQV.FPS
Retrocopy AFEGQVGQAAYSASKGG>IVGMTLPTAPPLAPTGIQVRATAPGLFDTLLLTCLPE<RVRNL*ASQVSFPS

Parental  RMGDPAEYAHLVQAIIENPFIN
          .MGDPAE..HL..AII.NPFI.
Retrocopy *MGDPAEHGHLI*AIIKNPFIS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_371 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_371 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371 ,
Ailuropoda melanoleuca	ENSAMEG00000013400	1 retrocopy	retro_amel_1352,
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,