RetrogeneDB ID: retro_amel_364

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192403.1:2015983..2016439(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL1
• Ensembl ID: ENSAMEG00000006519
• Aliases: None
• Description: derlin 1 [Source:HGNC Symbol;Acc:28454]

Sequence

>retro_amel_364
TTACTCTTGCTCCTCTTTAACTGGATTTGCTTCGTGATTACTGGCTTAGCAATGAATATGCAGCTGCTGACGGTTCCTCT
GATCATGTCGGTGGTTTATGTCTAGGCCCGGCTGCACAGAGATAGGATTGTATGGTTTTTGTGTGGAACACAAATTACGG
CCTGTTACTTACCATGGATTATCCTTAGATTCAACTATAACATGGGAGGCTCGGTGACCAATGAGCTCATTGGAAATCTT
GTTGGACATCTTTATTTCCTCCTAATGTTCAGCTACCCAATGGACTTGGGATGAAGACATTTTCTATCCACACCTGTTTT
TGCACTGCTGTCTGCCCAGCAGGAGAGGAGGGGTGTCAGGATTTGGTGTGCCCCCTGTAGCATGAGGCGAGTTGCTGATC
AGAATGGTGGAGGTGGGAGACACAACTGGGGACAGGACTTTCAGCTTGGGGACCAA

Alignment

ORF - retro_amel_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 60.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFMLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDMIVSFWFGTRFKACYLPWVILGFNYIIGG
          L..LLFNWIC.VITGLAM.MQLL..PLIMSV.YV.A.L.RD.IV.F..GT...ACYLPW.IL.FNY..GG
Retrocopy LLLLLFNWICFVITGLAMNMQLLTVPLIMSVVYV*ARLHRDRIVWFLCGTQITACYLPWIILRFNYNMGG

Parental  SVINELIGNLVGHLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSRRGGVSGFGVPPASMRRAADQNGGGG
          SV.NELIGNLVGHLYF.LMF.YPMDLG.R.FLSTP.F........R.GV......P.SMRR.ADQNGGGG
Retrocopy SVTNELIGNLVGHLYFLLMFSYPMDLG*RHFLSTPVFALLSAQQERRGVR-IWCAPCSMRRVADQNGGGG

Parental  RHNWGQGFRLGDQ
          RHNWGQ.F.LGDQ
Retrocopy RHNWGQDFQLGDQ

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_364 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_364 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006519	1 retrocopy	retro_amel_364 ,
Canis familiaris	ENSCAFG00000000974	1 retrocopy	retro_cfam_754,
Cavia porcellus	ENSCPOG00000011870	1 retrocopy	retro_cpor_1520,
Myotis lucifugus	ENSMLUG00000009085	1 retrocopy	retro_mluc_2035,
Mustela putorius furo	ENSMPUG00000001132	1 retrocopy	retro_mputfur_1082,
Mus musculus	ENSMUSG00000022365	1 retrocopy	retro_mmus_919,
Rattus norvegicus	ENSRNOG00000005551	2 retrocopies	retro_rnor_1206, retro_rnor_2717,
Sarcophilus harrisii	ENSSHAG00000011915	1 retrocopy	retro_shar_588,