RetrogeneDB ID: retro_amel_1379

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193287.1:626983..627448(-)
• Located in intron of: ENSAMEG00000010566

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000009433
• Aliases: None
• Description: None

Sequence

>retro_amel_1379
ATGGCAGAGCACGGTTACAGCTTTTGGCTGACTACATACAGCAAATGTAAACTTATCCAGATTGAATATGCTTTCACTGT
TGTAGTTGGAAGAGCCCCTCCAGTGGGAATTTAAGCTGCAAATAGTGTGATGTTAGCAACTGAGAAGAAACAATTCCATT
CTGTCTGATAAGCAAGGTGTAAACAAAGTGGAAGCAATTACTGAGCATGCAGGCTTGGTGTATACTGGCATGGGCCCAGA
TTACAGAGTGCTTGTGCACACAGCTCAAAAACTAGCTCAGCGGTACTGTCTCATTTACCAAGCATCCATTCTCGCAGCTC
AGCTGGATAGGGAGTAGCTTCTGTGATGCAAGAATATGCTCAGTCAGGTGGTGTTCATCCATTTGGAGTTTCTTTACTAA
TTTGTGGTTGGAATGAGGGGCAACTGTATTTATTTCAGTTAGATCCATCTGAAGCTCACTTTGCC

Alignment

ORF - retro_amel_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 67.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQK-SILYDERSVHKVEPIT
          MAE.GYSF.LTT.S...KL.QIEYA...V.G.AP.VGI.AAN..V.....K...SIL.D...V.KVE.IT
Retrocopy MAEHGYSFWLTTYSKC-KLIQIEYAFTVVVGRAPPVGI*AANS-VMLATEKKQ>SILSDKQGVNKVEAIT

Parental  KHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQR-VASVMQEYTQSGGVRPFGVSLLICG
          .H.GLVY.GMGPDYRVLVH.A.KLAQ.Y.L.YQ..I..AQL....VASVMQEY.QSGGV.PFGVSLLICG
Retrocopy EHAGLVYTGMGPDYRVLVHTAQKLAQRYCLIYQASILAAQLDRE<VASVMQEYAQSGGVHPFGVSLLICG

Parental  WNEGRPYLFQSDPSGAYFA
          WNEG..YLFQ.DPS.A.FA
Retrocopy WNEGQLYLFQLDPSEAHFA

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_1379 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1379 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 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009433	3 retrocopies	retro_amel_1029, retro_amel_1336, retro_amel_1379 ,
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Mustela putorius furo	ENSMPUG00000018145	1 retrocopy	retro_mputfur_548,
Mus musculus	ENSMUSG00000015671	4 retrocopies	retro_mmus_1104, retro_mmus_1105, retro_mmus_1215, retro_mmus_1320,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Otolemur garnettii	ENSOGAG00000016805	1 retrocopy	retro_ogar_197,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Rattus norvegicus	ENSRNOG00000049920	2 retrocopies	retro_rnor_2041, retro_rnor_2769,
Sus scrofa	ENSSSCG00000020769	3 retrocopies	retro_sscr_1082, retro_sscr_419, retro_sscr_440,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,