RetrogeneDB ID: retro_amel_588

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192513.1:2268013..2268319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30L
• Ensembl ID: ENSAMEG00000016695
• Aliases: None
• Description: SAP30-like [Source:HGNC Symbol;Acc:25663]

Sequence

>retro_amel_588
ATCCAGAGTGCATTAAATAGGAGGAAGAGGAAGACAAGTGACAATGACAGAAATTCTGAGCAGAATACTGTCATTCCTGA
GGTCGATCTGTTTCAGCTGCAGGTGAACACTCTGTGACATCCTAAATGACACTGTAATTTCCAGACTAGCCTGGGCTTCC
ATGAGGCCCAGTTAGCAGAAGCAGTCAGCTGACACTTCAGGAACTTAACTGTGAATGCAAAAGAGACCCTTGCCTACTTA
ATCTCCATGGTAAAGAGTAACAGGAGTAGAATGGACCAGACATTGAAGGGCAGCAAGCAGCTTGAG

Alignment

ORF - retro_amel_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.99 %
• Parental protein coverage: 88.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQSVRNKRKRKTSDDGGDSPEHDTDIPEVDLFQLQVNTLRRYKRHYKLQTRPGFNKAQLAETVSRHFRNI
          IQS..N.RKRKTSD....S.E..T.IPEVDLFQLQVNTL...K.H...QT..GF..AQLAE.VS.HFRN.
Retrocopy IQSALNRRKRKTSDNDRNS-EQNTVIPEVDLFQLQVNTL*HPK*HCNFQTSLGFHEAQLAEAVS*HFRNL

Parental  PVNEKETLAYFIYMVKSNKSRLDQKSDGSKQLE
          .VN.KETLAY.I.MVKSN.SR.DQ...GSKQLE
Retrocopy TVNAKETLAYLISMVKSNRSRMDQTLKGSKQLE

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_588 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_588 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016695	1 retrocopy	retro_amel_588 ,
Bos taurus	ENSBTAG00000004000	1 retrocopy	retro_btau_1024,
Canis familiaris	ENSCAFG00000017642	1 retrocopy	retro_cfam_2138,
Felis catus	ENSFCAG00000014985	1 retrocopy	retro_fcat_1968,
Mustela putorius furo	ENSMPUG00000013575	1 retrocopy	retro_mputfur_955,
Ochotona princeps	ENSOPRG00000014552	2 retrocopies	retro_opri_176, retro_opri_953,