RetrogeneDB ID: retro_amel_982

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192792.1:1376587..1377099(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSAMEG00000003965
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_amel_982
GTGAATATCGTCGGTTGGTTTGTCCAGTTCTTCAAGTCCATATAGGGCCTTCACTTTGAGACAGAGGGCCACCAGAAGCT
GGAAATGAACCATCCTTGTGTCATCATTTCTAACCACCAACGTGTCCTGAACATGATGGGCCACTTGGAGGCCCTCTGCA
AGTGCTATGTGTAGATCACCAAGCAGAAGTTCTCTTCATGGGGCCTGTAGACCTGATCTTGTGTCTCAGGGACATCTTTA
TCAACTGGCAGTGCTCCAGGACAAACAATGACTGGATGTCTGACATGGGCCAGCACATGGTCAGGAAGAACCTCAAAATG
TGGATCTACCCTGAGGATATGCAGAAGGACAATGGGGACCTGCTACCTTTAAGGAAAGATGCCTTTTACCTGGCAGTTCA
GGTCTAGGTGCCTATCATTTCTGTGGTGTATCCCACCTTCTTCTCTTTCTATGACCCCAAAAGGGAGCTCTTCCTCTTAG
GAACATTCAAGGTGGAGATGCTGGATACCATC

Alignment

ORF - retro_amel_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.8 %
• Parental protein coverage: 76.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRIIRWFVMKFKYVLGLRFETKGLQKLEVDHPCVIISNHQSILDMMGLMEALPERCVQVAKR-ELLFLGP
          ..I..WFV..FK...GL.FET.G.QKLE..HPCVIISNHQ..L.MMG..EAL....V...K..E.LF.GP
Retrocopy VNIVGWFVQFFKSI*GLHFETEGHQKLEMNHPCVIISNHQRVLNMMGHLEALCKCYV*ITKQ<EVLFMGP

Parental  VGLVIYLGGIFFINRQQSRTARTVMADVGERMVKDNLKVWIYPEGTRNDNGDLLPFKKGAFYLAIQTQVP
          V.L...L..IF.IN.Q.SRT....M.D.G..MV..NLK.WIYPE....DNGDLLP..K.AFYLA.Q..VP
Retrocopy VDLILCLRDIF-INWQCSRTNNDWMSDMGQHMVRKNLKMWIYPEDMQKDNGDLLPLRKDAFYLAVQV*VP

Parental  IIPVIYSSFSSFYNPKTKLFNSGTIKVEVLDAI
          II.V.Y..F.SFY.PK..LF..GT.KVE.LD.I
Retrocopy IISVVYPTFFSFYDPKRELFLLGTFKVEMLDTI

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_982 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_982 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003965	1 retrocopy	retro_amel_982 ,
Canis familiaris	ENSCAFG00000019569	1 retrocopy	retro_cfam_1838,
Equus caballus	ENSECAG00000010932	1 retrocopy	retro_ecab_825,
Felis catus	ENSFCAG00000011607	1 retrocopy	retro_fcat_1778,
Mustela putorius furo	ENSMPUG00000011249	1 retrocopy	retro_mputfur_1160,
Ochotona princeps	ENSOPRG00000003291	1 retrocopy	retro_opri_578,
Ictidomys tridecemlineatus	ENSSTOG00000023422	1 retrocopy	retro_itri_5,