RetrogeneDB ID: retro_amel_1275

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193135.1:545904..546311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000011230
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSAMEG00000009727
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_amel_1275
TGGGGGGCAGCCGGCATGTTATGCCACGTGGGAGCCCATGTCTTTCTCATTCATGATGACCACGACCCCCTCTTTGAAGA
TGGGTACACCCTCATCCCTGCTGTCATGATCATCCTGTAGGAGCCCTGCTTTTCCTTATTGGGCTACTTGGCTGCCGTGC
AGCAATCCCACACAGCCGCTGCGGACTTGCCATGTTTGTCATCAGTCTGCTCTTGGATTTTGTCACAGAAGTTGTTGTCA
TGGGTTGGGGATACGTTTACAGAGCAAAGGTGGAACATGAGGGTGATGGCGGCATTCAGAAAGTGTGTGAGACCTACACG
GGGACCAACACAGATGCTGCGACCCAGGTGGGTGGTTATGCACAGAGACAGCTGCAGTGCCATGGAGCTCACAGCTACTC
AGACTGG

Alignment

ORF - retro_amel_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WGAAGILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIA-VGALLFIIGLIGCCATIRESRCGLATFVII
          WGAAG.LC.VGA.VF...DD.D..FED.YTLIPAV.II..VGALLF.IGL.GC.A.I..SRCGLA.FVI.
Retrocopy WGAAGMLCHVGAHVFLIHDDHDPLFEDGYTLIPAVMIIL<VGALLFLIGLLGCRAAIPHSRCGLAMFVIS

Parental  LLLVFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASRAIDYVQRQLHCCGIHNYSDW
          LLL.FVTEVVV...GYVYRAKVE.E.D..IQKV..TY.GTN.DAA.....Y.QRQL.C.G.H.YSDW
Retrocopy LLLDFVTEVVVMGWGYVYRAKVEHEGDGGIQKVCETYTGTNTDAATQVGGYAQRQLQCHGAHSYSDW

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_1275 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1275 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275 ,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,