RetrogeneDB ID: retro_amel_715

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192585.1:1326949..1327663(+)
• Located in intron of: ENSAMEG00000017766

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011920
• Aliases: None
• Description: None

Sequence

>retro_amel_715
CAGAGCAGTCAAGAAAACAGTTTTTTTGGTGGTCTGAGCTTTGAACCTACACATGACAGTTTAAAAGAACATTCTGAAAA
ATGGGGAACACTTACGGAGTATGTGGTGATGAGAAATCCCCAAACAAAATGTTCCAAGGGTTTTGGTTTTATGACTTATG
CTTGTGTTGAAGAGGTGTATGCAGCAACCTGTGCTTGACCACACATGGTTGATGGGCCTGCACTGGAATCAAAGAGAGCT
ATTTCTAGAGAGGATTTTGTAAAGCTTGGTGCCCATCTCACAGTGAAGAAAATTTTCGTTGGTGGCATTAAAGAAGATAC
AGAAGAATATAATTTGAGAGACTATTTTGAAATGTATGGCAGGATTGAAACCAAAGAAATTATGGAAGAGAGGCAGAATG
GAAAAAAGAGAGGATTTGCTTTTGTAACTTTTGATGATCATGATAGAGTTGATCAAATTGTTGTTCAGAAATACCACACT
ATTAATGGGCGTAACTGTGAAGTGAAAAAGACCCTTTCTAAAAAAGAAAGGCCGTCTGCTGGATCACAAGACATCATGGA
GGTGGCTCTGGCAACTTGATGGGTTGTGGTGGAAACTTCTGTAGAAGAGGTAGCTATGGTGGTAGAGGTGGTGGCAGCAG
AGGTGCCTTATGGAGGAGGTGATGGTAGTAGATATAATGGATTTGGAATTGATGGTGGCAACCATGGTGGTGGT

Alignment

ORF - retro_amel_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 65.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPEQLRKLFIALSFETT--GLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHKV
          ...Q....F..LSFE.T...L.EH.EKWGTLT..VVMR.PQTK.S.GFGF.TY.CVEEV.AA.CA.PH.V
Retrocopy QSSQENSFFGGLSFEPTHDSLKEHSEKWGTLTEYVVMRNPQTKCSKGFGFMTYACVEEVYAATCA*PHMV

Parental  DGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFA
          DG...E.KRA.SRED.VK.GAHLTVKKIFVGGIKEDTEEYNLRDYFE.YG.IET.E.ME.RQ.GKKRGFA
Retrocopy DGPALESKRAISREDFVKLGAHLTVKKIFVGGIKEDTEEYNLRDYFEMYGRIETKEIMEERQNGKKRGFA

Parental  FVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQ-RGRGGGSGNFMGRGGNFGGGGNFGRG
          FVTFDDHD.VD.IVVQKYHTING.NCEVKK.LSK.E..SAGSQ.R..GGGSGN.MG.GGNF...G..G..
Retrocopy FVTFDDHDRVDQIVVQKYHTINGRNCEVKKTLSKKERPSAGSQ<RHHGGGSGNLMGCGGNFCRRGSYGGR

Parental  GNFGGRGG-YGGGGGGSRGSYGGGDGGYNGFG
          G..G.RG..YG.GG.GSR....G.DGG..G.G
Retrocopy GG-GSRGA>YG-GGDGSRYNGFGIDGGNHGGG

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_715 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_715 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 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726, retro_amel_547, retro_amel_925,
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715 , retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,