RetrogeneDB ID: retro_amel_272

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192372.1:1698058..1698489(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL26L1
• Ensembl ID: ENSAMEG00000011270
• Aliases: None
• Description: ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]

Sequence

>retro_amel_272
ATGAAGTTCAATCCCTTTGTGGCTTCTGACTGGAGCAAGAACCACAAAAGCTATTTCAATGCATCTTCCCACATTCGCAG
GAAGATTATGTCTTCCCCCTTTTTCCAAAGAGCTGAGACAGAAGTAAAGTGTTTAATCAATACCCATCTGAAAGGATGAT
GAAGTACAGGTTGTGCAAGGACACTACAAAGGTCAGCAAACTGGTAAAGTAGTCCAGGTTTACAGGAAGAAATGTGTAAT
CTACATTGAAGAGTACAACAAGAGAAGGCGAATGATACAACTGTCCATGTGGACATTCACCCTAGCAAGGTGGTTATCAC
TAGCCTAAATCTAGGCAAAGACTGCAAAAAATCCTTGACGGTAAAGTCAAATCTTGCCAAGTAGGAAAGGAAGAGGGCAA
ATTAAAGGAAGAAACAATTGAGAAGATGCAG

Alignment

ORF - retro_amel_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.83 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKFNPCVTSDGSKTRKRRFNAPSHVRRKIMSSPL-SEELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGK
          MKFNP.V.SD.SK..K..FNA.SH.RRKIMSSP..S.ELRQK..V.S.PI.KDDEVQVV.GHYKGQQ.GK
Retrocopy MKFNPFVASDWSKNHKSYFNASSHIRRKIMSSPF>SKELRQK*SV*SIPI*KDDEVQVVQGHYKGQQTGK

Parental  VVQVYRKKYVIYIE-RVQREKANGTTVHVGIHPSKVVITRLKLDKDRK-KILERKAKSRQFGKEKGKYKE
          VVQVYRKK.VIYIE.RVQ.EKAN.TTVHV.IHPSKVVIT.L.L.KD.K.KIL..K.KS.Q.GKE.GK.KE
Retrocopy VVQVYRKKCVIYIE<RVQQEKANDTTVHVDIHPSKVVITSLNLGKDCK<KILDGKVKSCQVGKEEGKLKE

Parental  ELIEKMQ
          E.IEKMQ
Retrocopy ETIEKMQ

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_272 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_272 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 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Ailuropoda melanoleuca	ENSAMEG00000011270	7 retrocopies	retro_amel_1106, retro_amel_1477, retro_amel_172, retro_amel_272 , retro_amel_560, retro_amel_788, retro_amel_887,
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5, retro_lcha_8,
Myotis lucifugus	ENSMLUG00000009799	1 retrocopy	retro_mluc_1556,
Tarsius syrichta	ENSTSYG00000001655	2 retrocopies	retro_tsyr_1805, retro_tsyr_759,