RetrogeneDB ID: retro_amel_6

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192344.1:3473879..3474929(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000020131
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TAF7L
• Ensembl ID: ENSAMEG00000009247
• Aliases: None
• Description: None

Sequence

>retro_amel_6
ATGAGTAAGAGCAAAGATGATGCTCCTCACGAACTAGAGAGCCAGTTTATCTTACGGCTCCCTCCGGAATACGCCTCTAC
TGTGAGGCGGGCAGTACAGTCTGGTCATGTCAACCTGAAGGACAGACTGACAATTGAGTTACACCCTGATGGACGTCACG
GGATCGTCAGAGTGGATCGGGTCCCGCTGGCCTCAAAATTGGTAGATCTGCCGTGTGTTATGGAAAGCTTGAAAACCATT
GATAAAAAAACGTTTTACAAGACAGCTGATATATGTCAGATGCTTGTCTCCACAGTTGATGGTGATCTCTATCCTCCTGT
GGAGGAACCAGTTGCTAGTACTGATCCCAAAGCAAGCAAGAAAAAGGATAAGGACAAAGAGAAAAAGTTTATATGGAACC
ATGGAATTACTCTGCCTCTAAAAAATGTCAGAAAGAGAAGGTTCCGGAAGACAGCAAAGAAGAAGTATATTGAATCTCCA
GATGTGGAGAAGGAAGTGAAGCGGTTGCTGAGTACAGATGCTGAAGCTGTGAGTACGCGTTGGGAGATAATTGCTGAAGA
TGAAACAAAAGAAACAGAAAATCAAGGCCTTGATGTCTCTTCTCCAGGAATGTCTGGTCACAGGCAGGGCCATGACTCAT
TAGAACATGATGAGCTTCGGGAGATATTCAATGACCTCAGCAGCAGCAGTGAAGATGAAGATGAGACTCAGCATCAAGAT
GAAGAAGATATAAACATCATCGACACTGAGGAAGATCTGGAAAGACAGCTACAGGACAAGCTGAATGAATCAGATGAACA
GCACCAAGAAAATGAGGGAACCAATCAGCTGGTTATGGGAATTCAGAAACAGATTGATAATATGAAAGGCAAACTCCAAG
AGACCCAGGATAGGGCAAAACGCCAGGAGGATCTCATCATGAAAGTGGAAAACCTCGCTCTCAAGAACAGATTTCAGGCT
GTGCTGGATGAACTCAAACAAAAGGAAGACCGAGAAAAGGAGCAGCTCAGTTCTTTGCAAGAAGAACTAGAATCACTCCT
AGAGAAGTGA

Alignment

ORF - retro_amel_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.15 %
• Parental protein coverage: 72.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSESQDEPPHELENQFILRLPPEHASTVRKIIRSGSVAMKDKLKIDLSSDGRHAVVEVEDVSLAAKVVDL
          MS.S.D..PHELE.QFILRLPPE.ASTVR....SG.V..KD.L.I.L..DGRH..V.V..V.LA.K.VDL
Retrocopy MSKSKDDAPHELESQFILRLPPEYASTVRRAVQSGHVNLKDRLTIELHPDGRHGIVRVDRVPLASKLVDL

Parental  PCVIGSLKTLDKKTFYKTADISQMLVCTADGDLHSPPEEQDTSTDLKVIGENEKEREKKYVWKHGITPPL
          PCV..SLKT.DKKTFYKTADI.QMLV.T.DGDL..P.EE...STD.K......K..EKK..W.HGIT.PL
Retrocopy PCVMESLKTIDKKTFYKTADICQMLVSTVDGDLYPPVEEPVASTDPKASKKKDKDKEKKFIWNHGITLPL

Parental  KNVRMKRFRKTTKKKYIESPDVEKEVKRLLCSDAEAVSARWEVIAEDETKEIESQG---SIPGFA-ISPG
          KNVR..RFRKT.KKKYIESPDVEKEVKRLL..DAEAVS.RWE.IAEDETKE.E.QG...S.PG......G
Retrocopy KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEIIAEDETKETENQGLDVSSPGMSGHRQG

Parental  MSDYKQDHISSEYGMLREVFSDSSSNSDEEDGDDE--DDEDDEDEDEEDEEDDDEYEVVEEE
          ......D........L.....D..........D....D.E.D......D..........E.E
Retrocopy HDSLEHDELREIFNDLSSSSEDEDETQHQDEEDINIIDTEEDLERQLQDKLNESDEQHQENE

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_6 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_6 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009247	1 retrocopy	retro_amel_6 ,
Bos taurus	ENSBTAG00000001979	1 retrocopy	retro_btau_107,
Loxodonta africana	ENSLAFG00000006941	1 retrocopy	retro_lafr_209,
Mus musculus	ENSMUSG00000009596	1 retrocopy	retro_mmus_72,
Oryctolagus cuniculus	ENSOCUG00000004497	1 retrocopy	retro_ocun_191,
Rattus norvegicus	ENSRNOG00000026315	1 retrocopy	retro_rnor_134,