RetrogeneDB ID: retro_amel_594

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192517.1:2240033..2240772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FADS1
• Ensembl ID: ENSAMEG00000016696
• Aliases: None
• Description: fatty acid desaturase 1 [Source:HGNC Symbol;Acc:3574]

Sequence

>retro_amel_594
CACATCAACAAGGTCCTTGTGAGAAAGTATATGAACTCTCTTCTAGCTTGGAGAACTGTCTCCAGAGCAGCCCAGTGTTA
AGCCTACTAAGAATAAAGAGCGAACAGATGATTTCCGGCAGCTGCAGACCATGGTGGAGCAGAAGGGGCTCAATGAAGGC
CAATCATGTCTTCTCTTGCTGTACCCACTCCACATCCTGTTGTGGGATGTAGCGGCCTGGTTCACTCTTTGGGTCTTTGG
AAGCTCCTTCCTGCCCCTCCTCCTCTGTACGCACTGTTTCACACAGTTCAGGCTCAAGCTGGCTGGCTGCAGCGTGACTT
TGGGCCTTGTCATTCTTCAGCACCTCTATGGAACCACCTGCTACATCATTTTGCAATTAGCCACCTGAAGGCAACCCCTG
GCAGGTGGCAGGATTACATGCACTTCCAGCTCCTCGACCCCAACTGCTTCTGCAAAGACCCAGATATCAACATGTACCCT
TTCTTCTTTGCCTCAGGGAAGATCCTCTCTGGGGAGCTTGGGACACCAGAAAAAAAAGTACATGCCTTACAACCACCGGC
ACAAATACTTCCCAACTGAGCCTCCAGCCTCGTTGCCTCTCTACTTCCACTGGCATTTTTTGCTATTTTGTTATCCAGCA
GAAAAACTGGATGGACTTACCTGCATGATCACATTCTACGCCAGTGTCTTCCTCACATAGGTGATGTTGTTGGGACCAAA
AGGCTTCCTGGTCAGGTTC

Alignment

ORF - retro_amel_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.06 %
• Parental protein coverage: 55.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  HINKGLVRKYMNSLL-IGELSPEQPSFEPTKNKELIDEFRELRATVEQMGL-MKANHVF-FLLHLLHILL
          HINK.LVRKYMNSLL..GELSPEQPS..PTKNKE..D.FR.L...VEQ.GL.MKANHVF..LL..LHILL
Retrocopy HINKVLVRKYMNSLL>LGELSPEQPSVKPTKNKERTDDFRQLQTMVEQKGL>MKANHVF<LLLYPLHILL

Parental  LDVAAWLTLWVFGTSLVPFLLCA-VMLSTVQAQAGWLQHDFGHLSVFSTSTWNHLLHHFVIGHLKGAPAS
          .DVAAW.TLWVFG.S..P.LLC......TVQAQAGWLQ.DFG.....S...WNHLLHHF.I.HLK..P..
Retrocopy WDVAAWFTLWVFGSSFLPLLLCT<ALFHTVQAQAGWLQRDFGPCHS-SAPLWNHLLHHFAISHLKATPGR

Parental  WWNHMHFQHHAKPNCFGKDPDINMHPLFFALGKILSVELGK-RKKKYMPYNHQHKYFFLIGPPALLPLYF
          W...MHFQ....PNCF.KDPDINM.P.FFA.GKILS.ELG......YMPYNH.HKYF....PPA.LPLYF
Retrocopy WQDYMHFQL-LDPNCFCKDPDINMYPFFFASGKILSGELGT>QXXXYMPYNHRHKYF-PTEPPASLPLYF

Parental  QWYIF-YFAIHRKKWVD-LAWMITFYVRLFLTYQPLLGLKGILGLF
          .W....YF.I..K.W.D.L..MITFY...FLT...LLG.KG.L..F
Retrocopy HWHFL>YFVIQQKNWMD<LTCMITFYASVFLT*VMLLGPKGFLVRF

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_594 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_594 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016696	1 retrocopy	retro_amel_594 ,
Equus caballus	ENSECAG00000023280	1 retrocopy	retro_ecab_493,