RetrogeneDB ID: retro_amel_1685

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193961.1:153762..153999(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MINOS1
• Ensembl ID: ENSAMEG00000003110
• Aliases: None
• Description: None

Sequence

>retro_amel_1685
CGTGTGGGGGACATGCCGGCTTCAGAGCTCGGCAGGAAGTGGGACCCGCGAGGGGCAGATGCCGTCGTGAAGCAGGTACT
GCTTTTGGATCACGACTTGTTTTCTCCCCCCTCAGCTTCTTTCAGAGGAGAATGTGGCCAATAGTCTTTGGTTCTGGCTT
GGGATTGGGAATGACCTACTCCAATTGTCAGCATGATTTCCAGGCTCCATTCTCTTCTACGTGGAAAATATGTCAAG

Alignment

ORF - retro_amel_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 88.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVGNMSDSELGRKWDRCMADAVVK-IGTGFGLGLVFS-LTFFKRRMWPLAFGSGMGLGMAYSNCQHDFQA
          RVG.M..SELGRKWD...ADAVVK..GT.FG..LVFS.L.FF.RRMWP..FGSG.GLGM.YSNCQHDFQA
Retrocopy RVGDMPASELGRKWDPRGADAVVK<AGTAFGSRLVFSPLSFFQRRMWPIVFGSGLGLGMTYSNCQHDFQA

Parental  PY-LLHGKYVK
          P..LL.GKYVK
Retrocopy PF>LLRGKYVK

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_1685 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1685 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003110	3 retrocopies	retro_amel_1685 , retro_amel_502, retro_amel_689,
Felis catus	ENSFCAG00000003066	2 retrocopies	retro_fcat_1448, retro_fcat_739,
Gallus gallus	ENSGALG00000004039	1 retrocopy	retro_ggal_19,
Loxodonta africana	ENSLAFG00000016199	1 retrocopy	retro_lafr_825,
Mus musculus	ENSMUSG00000050608	1 retrocopy	retro_mmus_2357,
Rattus norvegicus	ENSRNOG00000042696	2 retrocopies	retro_rnor_16, retro_rnor_2460,
Sus scrofa	ENSSSCG00000028414	1 retrocopy	retro_sscr_1171,
Tupaia belangeri	ENSTBEG00000004024	1 retrocopy	retro_tbel_4339,
Vicugna pacos	ENSVPAG00000011525	1 retrocopy	retro_vpac_607,