RetrogeneDB ID: retro_amel_547

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192495.1:2318757..2319608(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1
• Ensembl ID: ENSAMEG00000000717
• Aliases: None
• Description: None

Sequence

>retro_amel_547
ATGTCTAAATCAGAGTCTCCCTAAGAACCTGAACATCTGTGGAAGTTCTTTATCAGAGGTTTGAGCTTTGAAAGAACCAG
TGAGAGTCTGAGGAGCCATGCTGAGCGATGGAGAACACTTATGGACTGTGTGGTAATGAGAGATCCCAACACTAAGCACT
CCAGAGGCTCTGGGTTTGTCCTCTGTGCCACCGTGGAGGACGTAGAGGCAGCCAAGAATGTAAAGCCACACAAAGTGGAT
GGAAGCGTTGTAGAACCAAAGAGGGCTGTCTCAAGAGAAGACTCTCAAAGTCCTGGTGTCCACTTAACTGTGAAAACGAT
TTTTGTTCATGGCATTAAAGACACTGAAGAACATCATCTAAGAGATTATTTGGAATAGAATGGGAAAATTGAAGTGATTG
AAATCATGACTGACTGAGGCAGTGGCAAAAAGAGAAGCTTTGCTTTTTAACATTTGACAGCCATGACTCTGTAGACAAGA
TTGTCATTCAAAAATACCATACTGTGAATGGCCACAACTGGGAAGTAAAGAAAACCCTATCTAAGCAAGAGATGGGTAGC
GTTTCATCCACCCAAAGAAGTTGAAGTGGTTTGGGAAAACTTGGTGGTGGCCATGGAGGTGGTTTTGGTGGGAACGACAA
CTTTGGTCATGGAGAAAACTTCCATGGGTGAGGTGGCTGTGGTGGCAGTCAAGGTGGTGGCAGATATGGTGGCCGTGGGG
ATGGCTACAATGGATTTGGGAATGATGGTGGTTATGGAGGAGGCGGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGA
AGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTACGGTGGGAGTGGC

Alignment

ORF - retro_amel_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.67 %
• Parental protein coverage: 76.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSESP.EPE.L.K.FI.GLSFE.T.ESLRSH.E.W.TL.DCVVMRDPNTK.SRG.GFV..ATVE.V.A
Retrocopy MSKSESP*EPEHLWKFFIRGLSFERTSESLRSHAERWRTLMDCVVMRDPNTKHSRGSGFVLCATVEDVEA

Parental  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR
          A.N..PHKVDG.VVEPKRAVSREDSQ.PG.HLTVK.IFV.GIK.DTEEHHLRDY.E..GKIEVIEIMTD.
Retrocopy AKNVKPHKVDGSVVEPKRAVSREDSQSPGVHLTVKTIFVHGIK-DTEEHHLRDYLE*NGKIEVIEIMTD*

Parental  GSGKKRGFAF-VTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
          GSGKKR.FAF..TFD.HDSVDKIVIQKYHTVNGHN.EV.K.LSKQEM.S.SS.QR..SG.G..GGG.GGG
Retrocopy GSGKKRSFAF<LTFDSHDSVDKIVIQKYHTVNGHNWEVKKTLSKQEMGSVSSTQRS*SGLGKLGGGHGGG

Parental  FGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYDSYNN
          FGGNDNFG.G.NF.G.GG.GGS.GGG.YGG.GDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGY.....
Retrocopy FGGNDNFGHGENFHG*GGCGGSQGGGRYGGRGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGS

Parental  GGGGGG
          G.GG.G
Retrocopy GYGGSG

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_547 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_547 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 8 parental genes, and 22 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,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,