RetrogeneDB ID: retro_amel_552

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192496.1:1470052..1470561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP3B
• Ensembl ID: ENSAMEG00000005118
• Aliases: None
• Description: nipsnap homolog 3B (C. elegans) [Source:HGNC Symbol;Acc:23641]

Sequence

>retro_amel_552
GGCCCCAGACAATATGATGGAATACTCTATGAGTTTCATACTTAATGTCTTAAACCTTTAAAGACAGATGAGTTTCCAGA
AAATATTATGAAAACCATTCATCTTTGGACAGCTGACTCTGATTTGGTTGGATTCAGGAGTGGAGGCAGAGTGAATAAAG
TGTTTCATGTTTGAAAGGATGATAGTTTTGCTCATGGAACTGAAGTTCAGAAAGGCTTGACCAAAAATAAAGAATGCCAA
GAACAATTTCTCGTTCCAGATTTGGCTCTCATTGATAAAGAAGAGTTTGAGATTACTTACGTGGTACCATGGTCCAAAAC
AGAAAAACCTCCAAAGGAGTCCATGAACTGGTTATTTTCCAGATGAAACCTGATGGGCCAACTCTGTGGGGTGATGCATC
TAAGAGGGCAGTTGGTGTCCCTGTAGACTTAAGCTACGTAAAACCAATTGGTGTTCTCCACCCAGAATATGGAGCGACCA
GCAGAGACTGTGTTCTTCGGTGAAATGAG

Alignment

ORF - retro_amel_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 70.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPRQYDGTFYEFRTYCLKPSKMNEFLENAKKYMHLRTAYSELVGFWSVEFGGQMNKAFHIWKYDNFAHRT
          GPRQYDG..YEF.T.CLKP.K..EF.EN..K..HL.TA.S.LVGF.S...GG..NK.FH..K.D.FAH.T
Retrocopy GPRQYDGILYEFHT*CLKPLKTDEFPENIMKTIHLWTADSDLVGFRS---GGRVNKVFHV*KDDSFAHGT

Parental  EVRKAVAKDKEWR-QILISNLALIDEQENEITYLVPWCKLE-KPAKEGVYELAIFQMKPGGPALWGDAFK
          EV.K...K.KE...Q.L...LALID..E.EITY.VPW.K.E.K..K.GV.EL.IFQMKP.GP.LWGDA.K
Retrocopy EVQKGLTKNKECQEQFLVPDLALIDKEEFEITYVVPWSKTE<KTSK-GVHELVIFQMKPDGPTLWGDASK

Parental  RAINAHVDLGYSKLVGVFHTEYGALNRVHVLWWNE
          RA....VDL.Y.K..GV.H.EYGA..R..VL..NE
Retrocopy RAVGVPVDLSYVKPIGVLHPEYGATSRDCVLR*NE

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_552 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_552 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Ailuropoda melanoleuca	ENSAMEG00000005118	1 retrocopy	retro_amel_552 ,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Equus caballus	ENSECAG00000008088	1 retrocopy	retro_ecab_978,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Mustela putorius furo	ENSMPUG00000007103	1 retrocopy	retro_mputfur_1471,