RetrogeneDB ID: retro_amel_1749

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194190.1:53228..53798(-)
• Located in intron of: ENSAMEG00000008187

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSAMEG00000001216
• Aliases: None
• Description: None

Sequence

>retro_amel_1749
CTGTTCAACCTAAAGTTCGCCGCCAAAGAACTCAGCAGGAGTGCCAAAAAATGCGACAAGGAGGAAAAGGCCGAAAAGGC
CAAGATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTGGCGAGGATACACGCCGAAAACGCCATTCGCCAGAAGAACC
AGGCGGTGAATTTCTTGAGAATGAGTGCGCGGGTCGATGCCGTGGCTGCCAGAGTCCAGACGGCGGTGACGATGGGCAAG
GTGACCAAGTCGATGGCCGGTGTGGTTAAGTCGATGGATGCGACGTTGAAGACTATGAATCTGGAGAAGATCTCAGCTTT
GATGGACAAATTTGAGCACCAGTTTGAGACGCTGGACGTCCAGACGCAGCAAATGGAAGACACGATGAGCAGCACGACTA
CGCTGACCACGCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGACGAGGCTGGCCTAGACCTCAACATGGAG
CTGCCGCAGGGGCAGACCGGCTCCGTGGGCACCAGCGTGGCTTCCGCCGAGCAAGATGAACTATCCCAGAGACTGGCCCG
CCTGCGGGAT

Alignment

ORF - retro_amel_1749 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.29 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAVAS
          LF.LKF.AK.L...AKK..K..KAE.AK.KKA.Q..N.E.AR..AENAIR.KN..VN.LRM..RVDAVA.
Retrocopy LFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVDAVAA

Parental  KVQTAVTMKGVTKNMAQVTKALDRALSTMDLQKVSAVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQE
          .VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.SA.MD.FE.Q...LDV.T..MED.MSS.TTLTTPQ.
Retrocopy RVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLTTPQN

Parental  QVDSLIVQIAEENGLEVLDQLSQLPEGASAVGESSMRSQEDQLSRRLAALRN
          QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy QVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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_1749 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1749 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749 ,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,