RetrogeneDB ID: retro_amel_1518

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193547.1:568692..569191(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf49
• Ensembl ID: ENSAMEG00000012481
• Aliases: None
• Description: chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128]

Sequence

>retro_amel_1518
CTCCTCTGGAAGAGGTGGCTGCTTGCCCTGCTCTCCGGGGTCTCGCTTGTCTACTTCCTCCTCAGCACCTTCAGGCAGGA
GGAGAGGGCAGTGAAAGATCAGAATCTCCTCCAGGTTCCAGACCATGACCAGCCCATTCTGGGGAAAGCGAAATTTCACC
TGGGCGAGAGCAGGCCGGCCTGGCCACCAGTGCCGGGACTCCATTCAAGGGAAGCACCTCGTCACCGACAGGCTGGGATG
CATTTGTGAGAGGGAGGATTTGCTGGTGAATGGCCGCTGGGACGTCAACGTCCCTGGAACAAAGCAGTACCTCCGTGACG
GCTGCTTGCCCCACGGCTGCTGCAGAGCTTCCAAGTACTGCATGTCCTGCTGCCTGCAGCCCAGCAAGTGACTTCTGGCA
CGCTTCCTCCCCTGGGCAGCCGTGGTGTTCCAGAACCTCTTCATGGATGTCGCAGATCACTTTGAATTGTATTTGGCCAA
ATGCAGGACCTCATCCCAG

Alignment

ORF - retro_amel_1518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 81.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRKRWVLALVFGLSLVYFLSSTFKQEERAVRDRNLLQVQDHDQPIPWKVQFHLGNS-SRPGNQCRNSIQ
          LL.KRW.LAL..G.SLVYFL.STF.QEERAV.D.NLLQV.DHDQPI..K..FHLG.S..RPG.QCR.SIQ
Retrocopy LLWKRWLLALLSGVSLVYFLLSTFRQEERAVKDQNLLQVPDHDQPILGKAKFHLGES>GRPGHQCRDSIQ

Parental  GKHLITDELGYICERKDLLVNGCCNVNVPGTKQYRCDGCLPHGCCGAYEYCVSCCLQPSKQLLLERFLNR
          GKHL.TD.LG.ICER.DLLVNG...VNVPGTKQY..DGCLPHGCC.A..YC.SCCLQPSK..LL.RFL..
Retrocopy GKHLVTDRLGCICEREDLLVNGRWDVNVPGTKQYLRDGCLPHGCCRASKYCMSCCLQPSK-*LLARFLPW

Parental  AAVAFQNLFMAVEDHFELCLAKCRTSSQ
          AAV.FQNLFM.V.DHFEL.LAKCRTSSQ
Retrocopy AAVVFQNLFMDVADHFELYLAKCRTSSQ

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_1518 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1518 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012481	2 retrocopies	retro_amel_1518 , retro_amel_1578,
Bos taurus	ENSBTAG00000047139	1 retrocopy	retro_btau_1667,
Callithrix jacchus	ENSCJAG00000009570	1 retrocopy	retro_cjac_1471,
Dasypus novemcinctus	ENSDNOG00000001294	9 retrocopies	retro_dnov_126, retro_dnov_1532, retro_dnov_1609, retro_dnov_1622, retro_dnov_1739, retro_dnov_2042, retro_dnov_2185, retro_dnov_2285, retro_dnov_232,
Echinops telfairi	ENSETEG00000016892	3 retrocopies	retro_etel_1064, retro_etel_1377, retro_etel_410,
Homo sapiens	ENSG00000111412	1 retrocopy	retro_hsap_4758,
Gorilla gorilla	ENSGGOG00000015690	2 retrocopies	retro_ggor_2963, retro_ggor_508,
Myotis lucifugus	ENSMLUG00000011912	1 retrocopy	retro_mluc_166,
Macaca mulatta	ENSMMUG00000018247	2 retrocopies	retro_mmul_2376, retro_mmul_2537,
Pan troglodytes	ENSPTRG00000005500	1 retrocopy	retro_ptro_2798,