RetrogeneDB ID: retro_amel_1231

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193074.1:235511..236260(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL16
• Ensembl ID: ENSAMEG00000014289
• Aliases: None
• Description: mitochondrial ribosomal protein L16 [Source:HGNC Symbol;Acc:14476]

Sequence

>retro_amel_1231
ATGTGGCAGCTGCTGACTTGAGCCAGGGGACCACTCCTGTGAGCAGCGTTGTCAGATTCTTGGGCAGCCCCACCTACCAT
TGCTGGGCTACAGATGCTGCTCCAGGAGGCAACTTTTGAAGATATTTCCATTCCTGAAAAGCCCAAGATTAGATTTGTTG
AAAGGGCACCATTTGTGCCAAAAGTGAGAAGAGAATCTAAAAACTTGACTGACATATATGGACCTTCTACTGAAGCTACT
GAGTTCACGGAAGGCAGTTTTTCAATCTTGGCACTTGGTGGTGGTTACCTCCATTGAGGCTGTTTTGAAATGGTGCGCCT
GACAATGAACCACTCTATGGACCCCAAGAACATGTTTGCCTTATGGAGAGTGCCAGCCCCTTTCAAGTGCATCACATGCA
AGGGTATGAGACAGCACATGGGGGAGGCAAAAGTGCCTTTGGCTACAACGTGACTCCTATGAAGGTTGGCCATCTCATTA
TAGAGATGGGTGGGCATTCTGAATTCAAAGAGTTACAACGTTTCCTTGACCAGGTTGCCCACAAATTGTCCTTCTCAGCA
AAAGCTGTGTGCATGAGACTCTAGAGAAGATGTGGAAAGATCAAGAGGAATGAGAATAGAACAACTGAAACCTCTAGATT
TTTGAGCAAGTAGCCACTGCCAAACCTGGGGATATGGAAAGTCCTGAGCCTGTATGACTTGACCCAGAAGGGGAGGTCCT
GGGGCAAATTCTATATGCCTGAATATGTG

Alignment

ORF - retro_amel_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MWRLLARAGAPLLRARPSDSWAAPPASAGLKMLLPVPTFEDVSIPEKPKLRFVERVPLVPKVRREPKNLR
          MW.LL..A..PLL.A..SDSWAAPP..AGL.MLL...TFED.SIPEKPK.RFVER.P.VPKVRRE.KNL.
Retrocopy MWQLLT*ARGPLL*AALSDSWAAPPTIAGLQMLLQEATFEDISIPEKPKIRFVERAPFVPKVRRESKNLT

Parental  DIRGPSTEATEFTEGSFAILALGGGYLHWGHFEMMRLTINRSMDPRNMFALWRVPAPFKPITRKGMGHRM
          DI.GPSTEATEFTEGSF.ILALGGGYLH.G.FEM.RLT.N.SMDP.NMFALWRVPAPFK.IT.KGM...M
Retrocopy DIYGPSTEATEFTEGSFSILALGGGYLH*GCFEMVRLTMNHSMDPKNMFALWRVPAPFKCITCKGMRQHM

Parental  -GGGKGAIDHYVTPVKAGRLIVEVGGRCEFKEVQGFLDQVAHKLPFPAKAVS-RETLEKMRKDQEEREQN
          .GGGK.A....VTP.K.G.LI.E.GG..EFKE.Q.FLDQVAHKL.F.AKAV...ETLEKM.KDQEE.E.N
Retrocopy <GGGKSAFGYNVTPMKVGHLIIEMGGHSEFKELQRFLDQVAHKLSFSAKAVC<HETLEKMWKDQEE*E*N

Parental  NQNPWTFEHIATA-NMLGIRKVLSPYDLTQKGRYWGKFYMPERV
          N.N...FE..ATA.N..GI.KVLS.YDLTQKGR.WGKFYMPE.V
Retrocopy N*NL*IFEQVATA>NL-GIWKVLSLYDLTQKGRSWGKFYMPEYV

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_1231 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1231 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014289	1 retrocopy	retro_amel_1231 ,
Canis familiaris	ENSCAFG00000031711	2 retrocopies	retro_cfam_393, retro_cfam_865,
Dipodomys ordii	ENSDORG00000015111	1 retrocopy	retro_dord_389,
Felis catus	ENSFCAG00000007540	2 retrocopies	retro_fcat_479, retro_fcat_639,