RetrogeneDB ID: retro_amel_637

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192540.1:1852325..1852896(-)
• Located in intron of: ENSAMEG00000006353

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000016433
• Aliases: None
• Description: None

Sequence

>retro_amel_637
GAGACAGAGGACCTACTCAGGAGTGATTTCTCCAAGAAGACTTCTGAGCTGGCAGCATTTGTAAAGGATCCAGCTCTCAA
TGAAGCTAACCTGAGCAATCTGAAGGCCCCTTTGGGTCTTCTGGTGCCTGATTCTGTGAAGGGGAAAGGGAAAGAAGAGC
AGAAGAAATTGCAGGAGAAGGAATAAATGGATTAAAAGATGAAAGGGCAAGCTGAAGGCCAAGGTTTTCCCAGTAGCCCA
GTGAACGGCAAGAAGATCATGATCCTCTTGTAGCACCTGACACCTGGGACTGAGGATGTCACTGGGCTATCAGCCTGGTC
CCTACCTGGCTACAGCTGCAGATACCTCAGATTGAGGATAGGATCAGTTTTGGAGTGTCTGTCTAGCAGGAGGTGTGTGA
GCTGATGACCACCCCTCAGCCCGAGCTGGAAGCCTCCCACACTCCAGTCTCCAAGGATTCCTCTGAATGGGGCAGTGTAG
CCAAGCAGTCCCATGGGTGCAATGATCTACAGCTCGTGTGCGAGCTGGATGAGGCAGAGTCGCAGGACTTTGGCTGGTGG
TCATGGAGATC

Alignment

ORF - retro_amel_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.07 %
• Parental protein coverage: 78.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTENLLGSYFPKKISELDAFLKEPALNEANLSNLKAPLDIPVPDPVKEKEKEERKKQQEKEDKDEKKKGE
          .TE.LL.S.F.KK.SEL.AF.K.PALNEANLSNLKAPL...VPD.VK.K.KEE.KK.QEKE..D.K.KG.
Retrocopy ETEDLLRSDFSKKTSELAAFVKDPALNEANLSNLKAPLGLLVPDSVKGKGKEEQKKLQEKE*MD*KMKGQ

Parental  DEDKGPPCGPVNCNEKIVVLLQRLKPEIKDVIE-QLNLVTTWLQLQIPRIEDGNNFGVAVQEKVFELMTT
          .E..G.P..PVN...KI..LL..L.P...DV......LV.TWLQLQIP.IED...FGV.V...V.ELMTT
Retrocopy AEGQGFPSSPVN-GKKIMILL*HLTPGTEDVTG<AISLVPTWLQLQIPQIEDRISFGVSV*QEVCELMTT

Parental  LHTKLEGFHTQISKYFSERGDAVTKAAKQPHVGDYRQLVHELDEAEYRD-IRLMVMEI
          ....LE..HT..SK..SE.G......AKQ.H.....QLV.ELDEAE..D...L.VMEI
Retrocopy PQPELEASHTPVSKDSSEWG----SVAKQSHGCNDLQLVCELDEAESQD<LWLVVMEI

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_637 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_637 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637 ,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,