RetrogeneDB ID: retro_amel_469

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192461.1:617255..617630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSAMEG00000009344
• Aliases: None
• Description: RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768]

Sequence

>retro_amel_469
GAGAGCCAGGACCGGCAACTGAAAATCGACGTGCTGGGGGACGGCACGTCCGGGAAGACCTCCGTAGCTACGTGTTTTGC
TCAAGAAACTTTTGGGAAACAGTACAAACAAACTATAGGACTGGATTTCTTTTTGAGAAGGATAACATTGCCAGGGAACT
TGAATGTTACTCTTCAAGTTTGGGATATAGGAGGACAGACAATAGGAGGCAAGATGTTGGATAAATATATCTATGGAGCA
CAGGGAATCCTCTTGGTATATGATATTACAAATTATTAAAGCTTTGAGAATTTAGAAGACTGGTATTCTGTGGTGAAGAA
AGTGAGCGAGGAGTCAGAAACTCAGCTATTGGTCGCCTTGGTGGGCAATAAAACA

Alignment

ORF - retro_amel_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.8 %
• Parental protein coverage: 85.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESQDRQLKIVVLGDGTSGKTSVATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQVWDIGGQTIGG
          ESQDRQLKI.VLGDGTSGKTSVATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQVWDIGGQTIGG
Retrocopy ESQDRQLKIDVLGDGTSGKTSVATCFAQETFGKQYKQTIGLDFFLRRITLPGNLNVTLQVWDIGGQTIGG

Parental  KMLDKYIYGAQGILLVYDITNYQSFENLEDWYSVVKKVSEESETQPLVALVGNKS
          KMLDKYIYGAQGILLVYDITNY.SFENLEDWYSVVKKVSEESETQ.LVALVGNK.
Retrocopy KMLDKYIYGAQGILLVYDITNY*SFENLEDWYSVVKKVSEESETQLLVALVGNKT

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_469 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_469 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009344	1 retrocopy	retro_amel_469 ,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tursiops truncatus	ENSTTRG00000003622	1 retrocopy	retro_ttru_697,