RetrogeneDB ID: retro_amel_720

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192587.1:1798282..1798707(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCFD2
• Ensembl ID: ENSAMEG00000006097
• Aliases: None
• Description: multiple coagulation factor deficiency 2 [Source:HGNC Symbol;Acc:18451]

Sequence

>retro_amel_720
TCTCTTTGGCTGTTCAAAACCCCTTTCCCATGTGGCCTGCTCTTGGCCTTTTAAGCTTCAGATGCCAGGGTTGAGGTGCC
TGGAGTGATCTTTTCCCATCCCGGTAGCGTGGGCCTGGATGAGAACACAGTGAATGACCAAAAGCATATCACGGAGTATC
TAAAAAGTGTCATCAACAAACCGGAGGCGGAGATGTCTCCACAAGAGCTACAGCTCCGTTATTTCAGAATGCTTGATTAT
GACGACAATAATTAGTGTTATGGCCTAGAACTTTCCACAGACATCACTCACATCCATAAGGAGGAGGATAATGAACAGGC
ACCACCAATGAGTGAAGCTGAACTGATTAACTTGATGGTGTTTTGAGAAAGGATGACAAGAACAATGATGAATACATTGA
CTATGCTGAATTTGCAAAATCACTG

Alignment

ORF - retro_amel_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 85.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLWLLRTPFLCGLLWAFCAPGARAEEPGASFSHPGSVGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQEL
          SLWL..TPF.CGLL.AF.A..AR.E.PG..FSHPGSVGLD.NTV.DQ.HI.E.L..VINKPEAEMSPQEL
Retrocopy SLWLFKTPFPCGLLLAF*ASDARVEVPGVIFSHPGSVGLDENTVNDQKHITEYLKSVINKPEAEMSPQEL

Parental  QLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGNEQAPPMSEAELINLI-DGVLRDDDKNNDGYIDYAEF
          QL.YF.M.DYD.NN...GLELST.ITH.HKEE.NEQAPPMSEAELINL.......DD.KNND.YIDYAEF
Retrocopy QLRYFRMLDYDDNN*CYGLELSTDITHIHKEEDNEQAPPMSEAELINLM<GVLRKDD-KNNDEYIDYAEF

Parental  AKSL
          AKSL
Retrocopy AKSL

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_720 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_720 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720 , retro_amel_906,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129, retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,