RetrogeneDB ID: retro_amel_1234

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193076.1:517528..517730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSAMEG00000010434
• Aliases: None
• Description: split hand/foot malformation (ectrodactyly) type 1 [Source:HGNC Symbol;Acc:10845]

Sequence

>retro_amel_1234
GAAAAAGTAGCTTGGGTAGACTTGGGTCTCTTAGAAGAGGACGACGCGTTCGAGGAGCTCCCTGAGGAAGACTGGGCTGG
TTTAGATGAAGATGAAGATGCACACGTTTGAGAGGATAATTGGGATGATGACAACACAGAGGACGACTTCTCCAGCCCGT
TAATGAGCTGAACTAGAGAAACATGGTTATAAGATAGAGACG

Alignment

ORF - retro_amel_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLR-AELEKHGYKMET
          EK...VDLGLLEEDD.FEE.P.EDWAGLDEDEDAHV.EDNWDDDN.EDDFS..L..AELEKHGYK.ET
Retrocopy EKVAWVDLGLLEEDDAFEELPEEDWAGLDEDEDAHV*EDNWDDDNTEDDFSSPLM>AELEKHGYKIET

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_1234 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1234 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010434	1 retrocopy	retro_amel_1234 ,
Equus caballus	ENSECAG00000018179	1 retrocopy	retro_ecab_360,
Erinaceus europaeus	ENSEEUG00000002237	2 retrocopies	retro_eeur_290, retro_eeur_586,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,
Sus scrofa	ENSSSCG00000015337	1 retrocopy	retro_sscr_67,
Ictidomys tridecemlineatus	ENSSTOG00000011501	1 retrocopy	retro_itri_253,
Tupaia belangeri	ENSTBEG00000016474	3 retrocopies	retro_tbel_2837, retro_tbel_2998, retro_tbel_3844,