RetrogeneDB ID: retro_amel_515

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192483.1:1924512..1924883(+)
• Located in intron of: ENSAMEG00000006666

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSAMEG00000017818
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_amel_515
GACACGGTAACTATCCAGACCAGGAAGTTCACGAGCAAGCAACTACTTCAGCGGAAACAAATGGTCACTGATGCTCTCCA
CCCCGGGAAGGCCACAGTAATTTAGGAACAACCAGCCACAGTGTACAAGACCACACCAGATGTCATCTTTGTATTTGGAT
TCAGAACTCATTTTGGTGGTGGCAAGACAACTGGCTTTGGCGTGATTTAGGATTCCTTGGATAACGCAAAGAAAAATGGA
CCTAAATACAGACTTGCAAGACATGACCGGTACGAGAAGAAAAAGACCTCCAGGAAACAGTGAAAGAACACAAAAGCAGA
ATGAAGAAAGTCACGGGGACAACAAGAGCCAGTGCTGGTGCTGGCAAACAG

Alignment

ORF - retro_amel_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.42 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGF
          DTVTI.TRKF....LLQRKQMV.D.LHPGKATV....I.E..A..YKTTPDVIFVFGFRTHFGGGKTTGF
Retrocopy DTVTIQTRKFTSKQLLQRKQMVTDALHPGKATV----I*EQPATVYKTTPDVIFVFGFRTHFGGGKTTGF

Parental  GMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQ-RKERKNRMKKVRGTAKANVGAGKK
          G.I.DSLD.AKKN.PK.RLARH..YEKKKTSRKQ..KE.K.RMKKV.GT..A..GAGK.
Retrocopy GVI*DSLDNAKKNGPKYRLARHDRYEKKKTSRKQ<VKEHKSRMKKVTGTTRASAGAGKQ

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_515 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_515 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 12 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515 , retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,