RetrogeneDB ID: retro_amel_1169

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192990.1:64300..64818(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGTA
• Ensembl ID: ENSAMEG00000005257
• Aliases: None
• Description: small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha [Source:HGNC Symbol;Acc:10819]

Sequence

>retro_amel_1169
AAGCGTTTGACCTATACCTCTCTACGTCAGGTTCCTGCGCACGCAGCTCTGGCACCTGGGGGACCCCCATCTGATCCCCA
GGACAGTTTGGAAGTTGCAATACAGTGCCTGGAGACTCCTTCTGGGCTGATGGTGTAAGGCAGGGGCCTAGCACTCCCTC
AGACGCTTCCGGAGTTATTTGAAGCAGCAGCCACAGGCAAGGAGGTGCCGCGGGACGTGAAGAACCCCAACAAACTCGGC
CTTCAGAGGAGTGCTAGGCCGAGACACAGTGTTCCCCAAACCGAAGGAAACGTAGAAAACGTTGAGGCTGCCGTGTACTT
CTACGGGAAAGCCGTTGAGCTGAACCTGGCCAACGCCATCTGTTTCTGTAACGGAGCCACGGCCTTCAGCAAACTCAGGA
GCTGCGTGGGGGCGGGGCAGGACTGTGAGCCGGCCAACTGCATAGACCCGTCCTAAACCAAACCCCGCGCGAAGCGAGCC
TCGCCCTCTCCAGTTCAAACGAGCACAGCCGAGCCCTT

Alignment

ORF - retro_amel_1169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.78 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRLAYAIIRFL--HDQLRHGGLSSDAQESLEVAIQCLETAFGVTVEDRDLALPQTLPEIFEAAAAGKEAP
          KRL.Y...R....H..L..GG..SD.Q.SLEVAIQCLET..G..V..R.LALPQTLPE.FEAAA.GKE.P
Retrocopy KRLTYTSLRQVPAHAALAPGGPPSDPQDSLEVAIQCLETPSGLMV*GRGLALPQTLPELFEAAATGKEVP

Parental  QDLRS-PEQAPPSEEDSAEAERL-KTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGN
          .D....P.Q..PSEE..AE......TEGN....VEN.EAAV.FYGKA.ELN.ANA..FCN.A.A.SKL..
Retrocopy RDVKN<PQQTRPSEEC*AETQCS>QTEGN----VENVEAAVYFYGKAVELNLANAICFCNGATAFSKLRS

Parental  YTGAVQDCERAICIDPSYSKAYGR-MGLALSSLNKHTEAV
          ..GA.QDCE.A.CIDPS..K.......LALSS.N.H..A.
Retrocopy CVGAGQDCEPANCIDPS*TKPRAK<ASLALSSSNEHSRAL

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_1169 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1169 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005257	1 retrocopy	retro_amel_1169 ,
Equus caballus	ENSECAG00000010381	2 retrocopies	retro_ecab_723, retro_ecab_780,
Monodelphis domestica	ENSMODG00000004900	1 retrocopy	retro_mdom_277,
Mus musculus	ENSMUSG00000004937	1 retrocopy	retro_mmus_621,
Sarcophilus harrisii	ENSSHAG00000011900	1 retrocopy	retro_shar_39,