RetrogeneDB ID: retro_amel_1376

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193282.1:43372..44406(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC41
• Ensembl ID: ENSAMEG00000009750
• Aliases: None
• Description: coiled-coil domain containing 41 [Source:HGNC Symbol;Acc:17966]

Sequence

>retro_amel_1376
GTCCACTTGTGTTAGAAATTAAAAGGTTTAGAAGAAGTAGCAGAATTAAGGGCTGAAAAAGAGAATTCTGATGCTCAGGT
AAGAAAATGTCCAAAGAATTCAGGCATGGCAGTTGGCTGAGATGCAGGCTACAGTCAGATCTCTTGAGGCTGAAAATCAG
TCAGCTAAACTCTTGGAAAAAGAGTTACAATCAAGCAATGAACAAAACACTGTGTTAATCAGTAAACTACGTAGAGCCAA
ACAGGAAATAAATACAATGAGCAGTAAAGTACAAGAACTTAAACATTCAAACAAATTTGAAATAACAGACATCAAACTGA
AAGCATCAAGACCTAAGAGTGAGCTAGAAAGAGAAAGGAGTAAGATTCAAAGTGAACTAAATGGAATACAGTCAGACAAT
TAAATTCTCAATTCAGGCTTTGAACACCACAAAGTGCTCCTGGTAGAAAAGGATCATGAATGAATATATTAAGTTCAACT
GCCAAGGAAGAAGGTTATCAAAAATCTGTGGTATTATAAGATAAAAAGCTGAACCTGGAAACAGATTAGTGGATTCAGAG
AAAATGAAAATGGAACATGATGTATGAAGGCGATCTGAAAAGGCTGAGTGTGAAGAGAAATTGCGGGCTTCACAGATGGC
AGAAGAGCCAGCCAGAAGGGAACTTCAAAGTATTAGGTTAAAACTTCAACAACAAATTATGAATATTGAAAATGCAGAGA
AAGAAAAAAATGAAAATTCTGACCTGAAACAGCAAATCTAGTAGTCTGAAGATCCAAGTGACCTTGCTTGCATAGTCAGA
GAATGAGTTGCTGAATTCAAACAAAATACTGAAGGAAATGATGGCGAGGTTTAAAACAGGATGCTGAAATTCAAGAAGCT
ACGCTGAAAAACCACAACTAGAAGTTGAAAAGTCATTGGAAGAGAAATGATACAATGATTGGAAGCAAAGCATGAGCTTC
AGGAATGTATCACTGACAGAGTAGAAAAGTATAATCACGCTAAAGAAAAACTGCAATGAGCTGCAACTGCCCAG

Alignment

ORF - retro_amel_1376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.34 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LHLSQKLKSLEAEVAELRAEKENSGAQV-ENVQRTQVRQLAEMQATVRSLEAEKQSAKLQAERLEKELQS
          .HL..KLK.LE.EVAELRAEKENS.AQV.ENVQR.Q..QLAEMQATVRSLEAE.QSAKL....LEKELQS
Retrocopy VHLC*KLKGLE-EVAELRAEKENSDAQV>ENVQRIQAWQLAEMQATVRSLEAENQSAKL----LEKELQS

Parental  SSEQNTVLISKLHKAEREVNTLTSKVKELKHSNKLEITDIKLEAARAKSELERERNKIQSELDGLQSDNE
          S.EQNTVLISKL..A..E.NT..SKV.ELKHSNK.EITDIKL.A.R.KSELERER.KIQSEL.G.QSDN.
Retrocopy SNEQNTVLISKLRRAKQEINTMSSKVQELKHSNKFEITDIKLKASRPKSELERERSKIQSELNGIQSDN*

Parental  ILKSAVEHHKALLVEKDRELIRKVQ-AAKEEGYQKLVVLQDEKIELE-NRLADLEKMKVEHDVWRQSEKD
          IL.S..EHHK.LLVEKD.E.I..VQ..AKEEGYQK.VVL.D.K..LE.NRL.D.EKMK.EHDV.R.SEK.
Retrocopy ILNSGFEHHKVLLVEKDHE*IY*VQ<TAKEEGYQKSVVL*DKKLNLE<NRLVDSEKMKMEHDV*RRSEKA

Parental  QCEEKLRASQMAEESARRELQSIRLKLQQQIVNIENAEKEKNENSDLKQQI-SSLQIQVTSLAQSENELL
          .CEEKLRASQMAEE.ARRELQSIRLKLQQQI.NIENAEKEKNENSDLKQQI.SSL.IQVT.LA.SENELL
Retrocopy ECEEKLRASQMAEEPARRELQSIRLKLQQQIMNIENAEKEKNENSDLKQQI>SSLKIQVTLLA*SENELL

Parental  NSNQMLKEMVERLKQECRNLRSQAEKAQLEVERTLEEK-QIQWLEEKHKLQERITDREEKYNQAKEKLQR
          NSN..LKEM..R.K..C.N.RS.AEK.QLEVE..LEEK..IQ.LE.KH.LQE.ITDR.EKYN.AKEKLQ.
Retrocopy NSNKILKEMMARFKTGC*NSRSYAEKPQLEVEKSLEEK<MIQ*LEAKHELQECITDRVEKYNHAKEKLQ*

Parental  AAIAQ
          AA.AQ
Retrocopy AATAQ

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_1376 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1376 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009750	1 retrocopy	retro_amel_1376 ,
Callithrix jacchus	ENSCJAG00000002860	1 retrocopy	retro_cjac_1662,
Cavia porcellus	ENSCPOG00000008997	1 retrocopy	retro_cpor_1537,
Rattus norvegicus	ENSRNOG00000007859	1 retrocopy	retro_rnor_384,