RetrogeneDB ID: retro_amel_945

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192764.1:736937..737170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP12
• Ensembl ID: ENSAMEG00000014554
• Aliases: None
• Description: fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]

Sequence

>retro_amel_945
GAGATCTTCTTTAAGCTGAGAGAAGAATTTGAAGAAACTGTACAAGCTGGCCAGAACACCAGGAGTACAGTAACCTTAGA
TAATGACCCCTTGATTTAGGTGCAGGCCTGGGCTGGGAAGGCGACCCCCATAAGGAGAAAGTTGGTGGATGGGAAAATGG
GGGTGGAAAGTACCATGAACAATGTTACCTGCACCAGCACATATGAGAGAGTATAAAAAACTCGAGCTCAAAC

Alignment

ORF - retro_amel_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.29 %
• Parental protein coverage: 55.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EISFKLGEEFEETTPGGHKTKSVITFDKDSLIQVQDWDGKENTIRRKLVDGKLVVESAMNNVICTRTYKR
          EI.FKL.EEFEET...G..T.S..T.D.D.LI.VQ.W.GK...IRRKLVDGK..VES.MNNV.CT.TY.R
Retrocopy EIFFKLREEFEETVQAGQNTRSTVTLDNDPLI*VQAWAGKATPIRRKLVDGKMGVESTMNNVTCTSTYER

Parental  V-QTNSNSN
          V...NS.SN
Retrocopy V<IKNSSSN

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_945 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_945 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945 ,
Ailuropoda melanoleuca	ENSAMEG00000014619	1 retrocopy	retro_amel_1139,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,