RetrogeneDB ID: retro_amel_1408

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193335.1:348710..349182(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSAMEG00000001047
• Aliases: None
• Description: None

Sequence

>retro_amel_1408
GTGCCCAAGAGGGGCTGAATGGCCAGTTATGATCTCCTTTTCCAGGAGGCGGTGATGGTGGCCAGGAAGGATGTCCGCAT
GCCTGAACACCTGAGCTGGCAGACAAGAGTGGGCCCAGTCTTCACGTCGTGGAGGCTACGCAGCCTCTGAGGTCACGAGG
CTGTGTAGACAACAGTGGGCCTGGAGACATTTCTACTGGTACGTCACCACCGAGGGTGTCTGGTAGCTCTGTGATGACCT
CCACCCGCCCCCGAGAATGTGCTGCATGGCAGCCGTCCTCAGACGGGCGGCTCGGCCCCAAGTCTGGAGGGAGAGTGGCC
TCTAGCCTCACGGCAGGGGAAGTTGACAGGGACACCTGCCGACAAAGCACCGTGCCCACTGGTGCCCCCAGAAGGCTGAG
GCCAGGGCTGGGTCAGCCACTGAATTCCCTTTCAGAGGCAGGTTTGGTCCCGGATGTGGTCAGCTGCCTCAG

Alignment

ORF - retro_amel_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.12 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPKKNRIAIYELLFKEGVMVAKKDVHMPKH-PELADKNVPNLHVMKAMQSLKSRGYV-KEQFAWRHFYWY
          .PK....A.Y.LLF.E.VMVA.KDV.MP.H.PELADK..P.LHV..A.Q.L.SRG.V...Q.AWRHFYWY
Retrocopy VPKRG*MASYDLLFQEAVMVARKDVRMPEH<PELADKSGPSLHVVEATQPLRSRGCV<RQQWAWRHFYWY

Parental  LTNEGIQYLRDYLHLP-PEIVPATLRRSRPETGRPRPKGLEGERP-ARLTRGEADRDAYRRSAVPPGADK
          .T.EG...L.D.LH.P.PE.V...L..SRP.TG...P..LEGE.P...LT.GE.DRD..R.S.VP.GA..
Retrocopy VTTEGVW*LCDDLHPP<PENV---LHGSRPQTGGSAPS-LEGEWP<SSLTAGEVDRDTCRQSTVPTGAPR

Parental  -KAEAGAGSATEFQFRGGFGRGRGQPPQ
          .KAEA.AGSATEF.FRG.FG.G.GQ.PQ
Retrocopy <KAEARAGSATEFPFRGRFGPGCGQLPQ

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_1408 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1408 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 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001047	4 retrocopies	retro_amel_1408 , retro_amel_1706, retro_amel_446, retro_amel_890,
Canis familiaris	ENSCAFG00000001214	2 retrocopies	retro_cfam_1, retro_cfam_92,
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Felis catus	ENSFCAG00000015355	3 retrocopies	retro_fcat_1443, retro_fcat_1681, retro_fcat_1757,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mustela putorius furo	ENSMPUG00000003117	3 retrocopies	retro_mputfur_1347, retro_mputfur_1533, retro_mputfur_1579,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Otolemur garnettii	ENSOGAG00000001365	5 retrocopies	retro_ogar_2166, retro_ogar_2314, retro_ogar_2553, retro_ogar_415, retro_ogar_873,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,