RetrogeneDB ID: retro_amel_1425

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193358.1:197692..198071(+)
• Located in intron of: ENSAMEG00000005203

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN13
• Ensembl ID: ENSAMEG00000010524
• Aliases: None
• Description: tetraspanin 13 [Source:HGNC Symbol;Acc:21643]

Sequence

>retro_amel_1425
ATGGTTATTCTCTTACTCGTGTTTATTGTTCTGTTTTCTGTATGTCCTTGCTTAGCCCTGAACCAGGAACAACAGGGTCG
ACTTCCAGAAGGGGGCTGGAACAATGCAGTGAGGGCTCAAAATGACATCCCGGGAAATTTAAACTGCTATGGGTTTTGAA
GTTCTAACCCAAATGACACCTGTCTGGCCAGCTGTGTCCAAAGCAGCCTCGGGAGCTCACGTGTGCACCAATTATAGGAA
CATAGGCCAGAAAGTTCCGAGCTTTGCAGAGGGCTGGGGCGCTGGCCTCTTCCTCTGCTTTCCAGCCATCCTGGGTGTTT
GGCTGACTTACAGACGCAGGAACCGGAAAGATCCTTGTGCCGATCCTAGTGGAATCCTT

Alignment

ORF - retro_amel_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIILLLVFIVQFSVSCACLALNQEQQGQLLEVGWNNTASARNDIQRNLNCCGFRSFNPNDTCLASCVKSS
          M.ILLLVFIV.FSV.C.CLALNQEQQG.L.E.GWNN...A.NDI..NLNC.GF.S.NPNDTCLASCV.SS
Retrocopy MVILLLVFIVLFSV-CPCLALNQEQQGRLPEGGWNNAVRAQNDIPGNLNCYGF*SSNPNDTCLASCVQSS

Parental  HPCS-LCAPIIG-KYAGEVLRFVGGIG--LFFSFTEILGVWLTYRYRNQKDPRANPSAFL
          ...S..CAPIIG......V..F..G.G..LF..F..ILGVWLTYR.RN.KDP.A.PS..L
Retrocopy LGSS<TCAPIIG<NIGQKVPSFAEGWGAGLFLCFPAILGVWLTYRRRNRKDPCADPSGIL

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_1425 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1425 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010524	1 retrocopy	retro_amel_1425 ,
Loxodonta africana	ENSLAFG00000005956	3 retrocopies	retro_lafr_1088, retro_lafr_195, retro_lafr_556,
Ictidomys tridecemlineatus	ENSSTOG00000008833	1 retrocopy	retro_itri_1367,
Tursiops truncatus	ENSTTRG00000009870	1 retrocopy	retro_ttru_551,