RetrogeneDB ID: retro_amel_488

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192472.1:2494889..2495746(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011042
• Aliases: None
• Description: None

Sequence

>retro_amel_488
GCCATGCATGAGTGCATCTCCATCCATGTTGGTCAGGCTGGTGTGCAGATGGGCATTGCCTGCTGGGAGTTCTCTTGCCT
GGACCATGGCATCCAGCTCAGCATTCAGATGCCAAGTGACAAGACAAATGGAGGAGGAGATGACTTTGGCATCTCCTTCA
GTGAGACATGTTCTGGCAAGCTGGTCCCCAAGGGCACTGTTTGTAAATCTGGAACCCACCGTCACTGATGAATTTCACAC
CGGCATCTACCACTAGCTCTTTATACTCTGAGGGGCTTGTCACAGACAAGGAAGATGCTGCCAATAACTGTGCCTGAGGG
TGCTACACTGTTGGCAAGGAGATCATTGACTCTGTCTTGGACTGAATTTGGAAACTGGCTGACTGGTGCACAGGTCTTCA
GGGCTTCTTGGTTTTCCACCGCTTTGGAGGGGAAACTGGTTCTGAGTTCACCTCCCTGCTGATGGAACATCTCTTGGCCA
ATTATGGCAAGAAGTCCAAGTTGGAGTTCTCCATTTACCCAGCCCCTCAAGTTTCCACAGCTGGAGTTGAGCCCTACACC
TCCATCCTCACTACCTACACCACCCGGGAGTACTGTGATTGTGCCTTCACGGTAGGCAATGAGGTCAGCTATGAAGTCTG
CCATAGAAACCTCTATATTGAATGCTCAGCCTACTCTAACCTTCACTGCCCTGTTGGCCAGATTGCGTCTTCCATCACTG
TTTCCCTCAGATGTGATGGAGCCCTGAATGTTGATCTGACAGAATTTCTGACCAACCTGGTGCCCTATCCCCACATCCAC
TTCCCTCTGGCCACATAGGCCCTTGTCGTCTCTGCTGAGAAAGCCTACCATCAACAG

Alignment

ORF - retro_amel_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 63.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVP-RAVFV
          ...ECISIHVGQAGVQ.G.ACWE..CL.HGIQ...QMPSDKT.GGGDD.F...FSET..GK.VP.RA.FV
Retrocopy AMHECISIHVGQAGVQMGIACWEFSCLDHGIQLSIQMPSDKTNGGGDD-FGISFSETCSGKLVP>RALFV

Parental  DLEPTVVDEVRTGTYRQLF-HPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKLADLCTGLQGFLI
          .LEPTV.DE..TG.Y..LF...E.L.T.KEDAANN.A.G.YT.GKEI.D.VLD.I.KLAD.CTGLQGFL.
Retrocopy NLEPTVTDEFHTGIYH*LF>YSEGLVTDKEDAANNCA*GCYTVGKEIIDSVLD*IWKLADWCTGLQGFLV

Parental  FHSFGGGTGSGFASLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
          FH.FGG.TGS.F.SLLME.L...YGKKSKLEF.IYPAPQVSTA.VEPY.SILTT.TT.E..DCAF.V.NE
Retrocopy FHRFGGETGSEFTSLLMEHLLANYGKKSKLEFSIYPAPQVSTAGVEPYTSILTTYTTREYCDCAFTVGNE

Parental  AIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS
          ..Y..C.RNL.IE...Y.NL....GQI.SSIT.SLR.DGALNVDLTEF.TNLVPYP.IHFPLAT.A.V.S
Retrocopy VSYEVCHRNLYIECSAYSNLHCPVGQIASSITVSLRCDGALNVDLTEFLTNLVPYPHIHFPLAT*ALVVS

Parental  AEKAYHEQ
          AEKAYH.Q
Retrocopy AEKAYHQQ

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_488 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_488 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488 , retro_amel_518,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,