RetrogeneDB ID: retro_amel_206

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192353.1:1611913..1612333(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSAMEG00000015774
• Aliases: None
• Description: synaptosomal-associated protein, 23kDa [Source:HGNC Symbol;Acc:11131]

Sequence

>retro_amel_206
ATGAATCACCCATCATCAGAAGAAATTCAACTGAGGGCTCACCAGGTTATGGACGGGTCTCTGGAAAATTCAAGAAGAAT
CCTGGGTTTAACCATTGAGTCTCAGGATGTAAGAGTCAAGACTAACACTATGCTGGATGAATAAGGGGTGCAAATAAACC
ATATACAAGAAGACATGGACCAAGTAAGTAGAGACGTGAGAGAGGCAGAGAAAATGTTAGCAGGACTCAATGGGTGCTGT
GGCCTTTGTGTCTGCCCATGTAACAAGATAAAGAAGATCGAGGCTGGTAAGGCTCATAAGGCAACATAGAGAGATGGCAG
AGACAACTCTTCTAGCAGTGTAATATCTAAGCAGCCAGGCCATGTGACAAATGGTCAGCCTCAGCAAACAACCATAAGAG
CCATCAATGGCAGATACATA

Alignment

ORF - retro_amel_206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 66.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDNLSSEEIQLRAHQVTDESLESTRRILGLALESQDAGIKTITMLDEQGEQLNRIEEGMDQINKDMREAE
          M...SSEEIQLRAHQV.D.SLE..RRILGL..ESQD...KT.TMLDE.G.Q.N.I.E.MDQ...D.REAE
Retrocopy MNHPSSEEIQLRAHQVMDGSLENSRRILGLTIESQDVRVKTNTMLDE*GVQINHIQEDMDQVSRDVREAE

Parental  KTLTELNKCCGLCVCPCNRTKNFESGKAYKSTWGDGGDNSPSDVVAKQPGRVTNGQPQQPATGAASGGYI
          K.L..LN.CCGLCVCPCN..K..E.GKA.K.T..DG.DNS.S.V..KQPG.VTNGQPQQ....A..G.YI
Retrocopy KMLAGLNGCCGLCVCPCNKIKKIEAGKAHKAT*RDGRDNSSSSVISKQPGHVTNGQPQQTTIRAINGRYI

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_206 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_206 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206 ,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,