RetrogeneDB ID: retro_amel_1467

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193441.1:69210..69678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000006651
• Aliases: None
• Description: None

Sequence

>retro_amel_1467
ATGGGTGTACAGACAGTCTTCTGCAGTACTAAGGACACGCTCCCGGGGTCCCTATCCCAAGACTCCAGAAGAACTAGCTG
CACTGCCACAAAAGTATAATATGTGGATGGAAAACTAGAAGCAGTACCTGGTTGATGGCGTGGAGTGTGGTGATTACCAG
AACCTCCCTGAGCCTCGCAGCAGGCGAGTGGCCCATGGTATGACTCGGTTTACCCACACCTGAGGTTGAGCTGGGTTGAA
CTGACGTACTGGGATCTAGACACACAATCAGGAACCTTGAGGCCACACACCCCCACCCCCACTGTTTTGGAATCTAATGT
GTAAGCAGCTCCTTGGCTTCCTGACCTTCATGCCAGTTCATGTTTTGGGTAGGGGAGAATTACCCCATCTACCAGCCTGT
GGAGCCAAAGCTGTATCCTCGTGCTCATCTGTATCTGGAACTCAGAGGCTGATCCCACCAAAGAGCCT

Alignment

ORF - retro_amel_1467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.0 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LGARTASHITKDMLP-GPYPKTPEERAAAAKKYNMRVEDYQPYPDDGMGYGDYPKLPD-RSQQERDPWYN
          .G..T....TKD.LP.GPYPKTPEE.AA...KYNM..E....Y..DG...GDY..LP...SQQ...PWY.
Retrocopy MGVQTVFCSTKDTLP>GPYPKTPEELAALPQKYNMWMEN*KQYLVDGVECGDYQNLPE<ASQQASGPWYD

Parental  WDHPDLRLNWGEPMHWDIDMYIRNRVDTSPT-PVSWNLMCKHLFGFVAFM-LFMFWVGETYPTYQPVGPK
          ...P.LRL.W.E...WD.D..........PT.P..WNLMCK.L.GF..FM..FMFWVGE.YP.YQPV.PK
Retrocopy SVYPHLRLSWVELTYWDLDTQSGTLRPHTPT>PLFWNLMCKQLLGFLTFM>QFMFWVGENYPIYQPVEPK

Parental  QYPYNNLYLERGG-DPTKEP
          .YP...LYLE..G.DPTKEP
Retrocopy LYPRAHLYLELRG>DPTKEP

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_1467 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1467 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 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467 , retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539, retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,