RetrogeneDB ID: retro_amel_1017

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192832.1:275740..276286(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSAMEG00000011877
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_amel_1017
GAAGAGGAGCTGGACCATGCCCTGCAAAAGCTGGAGGAAGCCGAGAAAGCTGCTGATGGAAGTCAAGGGAGGTATGAAGG
TTACGGAAAACTAAGCCTTAAGAGATGAAGAAAATTGGAACTCCAGAAAATTCAACTCAAGCAAGCTGAGCACACTGCAG
AAGAAGCAGATCAGAAGTATGAAGGGGTGGCTCAGAAGTGGGTGATTACTGAGGGGGACCTGGAAGGCACAGGGAACAAG
CTGAGCTGGCAGACTCCCGTTGCCAGGCAGTGGATGAGCAGGTAAGACTGATGGACCAGAACCTAAAGTGTCTGAGTGCT
GCAGAAGGAAAATACTCTCAAAAGGGAGAGAAATATGAAGAAGAGATAAAGATTCTTACCGACAAACTCGAAACAGGCAG
AGACCCATGCTGAGTTTGCTGAGAGACTGGCAGCCAAGCTAGAGAGGATAACTGATGATTTGGAAGACAAGCTGAAATGC
ACCAAAGAGGAGAACCTCTGTACACAAAGGATGCCAGATCAGCTGCTGCCTGGCCTGAACGAGATG

Alignment

ORF - retro_amel_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QERLATALQKLEEAEKAADESER-GMKVIENRALKDEE-KMELQEIQLKEAKHIAEEADRKYEEVARKLV
          .E.L..ALQKLEEAEKAAD.S...GMKV.EN.AL.DEE.K.ELQ.IQLK.A.H.AEEAD.KYE.VA.K.V
Retrocopy EEELDHALQKLEEAEKAADGSQG>GMKVTEN*ALRDEE<KLELQKIQLKQAEHTAEEADQKYEGVAQKWV

Parental  IIEGDLERT-EERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKL-KEAETR
          I.EGDLE.T..E.AELA.SRC...DEQ.RLMDQNLKCLSAAE.KYSQK..KYEEEIKILTDKL.K.AET.
Retrocopy ITEGDLEGT<REQAELADSRCQAVDEQVRLMDQNLKCLSAAEGKYSQKGEKYEEEIKILTDKL>KQAETH

Parental  AEFAERSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AEFAER..AKLE...DDLEDKLKCTKEE.LCTQRM.DQ.L..LNEM
Retrocopy AEFAERLAAKLERITDDLEDKLKCTKEENLCTQRMPDQLLPGLNEM

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_1017 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1017 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 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011877	2 retrocopies	retro_amel_1017 , retro_amel_1212,
Bos taurus	ENSBTAG00000033217	3 retrocopies	retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus	ENSCPOG00000007279	1 retrocopy	retro_cpor_150,
Dasypus novemcinctus	ENSDNOG00000019156	7 retrocopies	retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus	ENSECAG00000010942	1 retrocopy	retro_ecab_390,
Felis catus	ENSFCAG00000012596	1 retrocopy	retro_fcat_1441,
Homo sapiens	ENSG00000143549	9 retrocopies	retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012, retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Myotis lucifugus	ENSMLUG00000013331	1 retrocopy	retro_mluc_1038,
Macaca mulatta	ENSMMUG00000010805	10 retrocopies	retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furo	ENSMPUG00000007875	1 retrocopy	retro_mputfur_604,
Mus musculus	ENSMUSG00000027940	1 retrocopy	retro_mmus_21,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,