RetrogeneDB ID: retro_amel_353

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192398.1:686365..686912(-)
• Located in intron of: ENSAMEG00000018255

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSAMEG00000008606
• Aliases: None
• Description: None

Sequence

>retro_amel_353
GTGATCAAGAATGTTCAAATCAAGAATGTTCAGAAGAATAATGGAAATGTGGAATTTTCAGAAAAAGAGTTGTCTGCTTT
GGTGAAACTTCCCTCCGGAGAGGATCACAATTTGAAACTGAGACTTCCTCATCCTATAACACCAGAACAGAGCACATTTA
AAGTACTTTCAACAAAGATTGAAATTAAAATGAAATCAAGACAGAGGCTGTACGATGGGAAAAGGTAAAGGGGCAAGGTG
ATGTGCCTAAACCAAAACAGTTCACAGCAGAAATAAGGAATTTATATCCATCATCACCTCATTATGCAAGAAATTGGGAT
AAATTGGTCAGTGAGATCAAAGAAGAAAAAATGAGAAGTTGGAGGGAGATGCTGCTTTAAACAAATTATTTCAGCAGATC
TATTCAGATGGTTCTGATGATATGAAACATGCCATGATCAAATCATTTACAGAGTCTGGTGGTACAGTTCTGAATACCAA
CTGGTCTGATGTAGGTAAAACGAAAGTTGAAATCAATCCTCCTGGTGATATGGAATGGAAAAAGTAC

Alignment

ORF - retro_amel_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.96 %
• Parental protein coverage: 60.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIITLMIKNVQKNNVNVEFSEKELSALVKLPSGEDYNLKLRLLHPVIPEQSTF-KVLSTKIEIKMK-KTE
          VI....IKNVQKNN.NVEFSEKELSALVKLPSGED.NLKLRL.HP..PEQSTF.K........K...KTE
Retrocopy VIKNVQIKNVQKNNGNVEFSEKELSALVKLPSGEDHNLKLRLPHPITPEQSTF>KYFQQRLKLK*N>KTE

Parental  AVRWEKLEGQGDMPKPKQFIADVKNLYPSSSHYTRNWDKLVGEIKEEE-KNEKLEGDAALNKLFQQIYSD
          AVRWEK..GQGD.PKPKQF.A...NLYPSS.HY.RNWDKLV.EIK.EE.KNEKLEGDAALNKLFQQIYSD
Retrocopy AVRWEKVKGQGDVPKPKQFTAEIRNLYPSSPHYARNWDKLVSEIK-EE<KNEKLEGDAALNKLFQQIYSD

Parental  GSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY
          GSD..K.AM.KSF.ESGGTVL.TNWSDVGK.KVEINPP.DMEWKKY
Retrocopy GSDDMKHAMIKSFTESGGTVLNTNWSDVGKTKVEINPPGDMEWKKY

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_353 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_353 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353 , retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,