RetrogeneDB ID: retro_amel_1445

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193378.1:417344..417751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL18
• Ensembl ID: ENSAMEG00000015398
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:HGNC Symbol;Acc:14477]

Sequence

>retro_amel_1445
GAAAAAGAAGCTTTTGATCGAGTGTTCACCAACCAGAACTCCCAGCATCTGGAGCTCGTAGCTGTAGCCAGGAAAGAGCA
GGGTCAGGGGACCATGTGGCCCTCTCCTGAGTTGCGAGTTTTAAAAGACTGAGCGTCATGTAGCAGCATTGTTGAGCTCT
GCAGTGGCTAGGTTGTGGTTTCGGTATCCACTCAGAATGGGCTATTAAGCACCTTTACAGCACCAAAAATGTGGTGGCCT
GTGAGAGTAAAGGATGAGTACTGGCAGAGCGATGCCTAGAGGCAGGACCCAGCTTCACGGTCTACCAGCCCACTCCTTGG
GAGGCAGCCTCAGACTCCATGAAATGACTACAGAGGGCCGTGAGAGAAGGTGGTGGGGTATTGCAGGAGCCTCAGAGAAT
CTATGAA

Alignment

ORF - retro_amel_1445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.36 %
• Parental protein coverage: 78.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENAAVAPEFTNRNPRNLELLGVARKERGWGTAWPSREFWHRLRVIR-TQHHVEAL-VEHHNGQVVVSAST
          E..A....FTN.N...LEL..VARKE.G.GT.WPS.E....LRV...T..HV.AL.VE...G.VVVS.ST
Retrocopy EKEAFDRVFTNQNSQHLELVAVARKEQGQGTMWPSPE----LRVLK>TERHVAAL<VELCSG*VVVSVST

Parental  R-EWAIKKHLYCTKNVVACESIGRVLAERCLEAGINFMVYQPTPWEAASDSMKRLQSAMTEGGVVLQEPR
          ..EWAIK.HLY.TKNVVACES.G.VLAERCLEAG..F.VYQPTPWEAASDSMK.LQ.A..EGG.VLQEP.
Retrocopy Q<EWAIK-HLYSTKNVVACESKG*VLAERCLEAGPSFTVYQPTPWEAASDSMK*LQRAVREGGGVLQEPQ

Parental  RIYE
          RIYE
Retrocopy RIYE

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_1445 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1445 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445 ,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,