RetrogeneDB ID: retro_amel_1706

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194019.1:264783..265270(+)
• 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_1706
ATGTTGAAGACCCAGATGAACCCTACTGTCATTTATGAACTCCTTTTCGAGGAAGGAGTGATGGTGGCCAAAAAGGATGT
CCACATGCCTAACACCTTGATCTGGCAGACAGGAACATACCCAATCTTTCACGTCTTCAAGGCCACGCAGTCTCTCAAAT
CATGAGGCTACGTAAAGGAATACATTGCCTAGAGACATTTCTACTGGAACCTTACCAATGAGGGTATCCAGTATCTCTGT
GATTACCTCCACCCACCCCCTGGATTGTGCCTGCCATTCTGCACCACAGCAGTCTTGAGACTGAAAGGCCACAGTCCAAA
GGTCTGAAGGGAGAGCCACCCACAAGACACACAGGGGAAGCTAACAGAAACACCTACAAAGTGCTGTGTCCCTTGGGGCT
GACAAGAAAGCTGAGGTTGGGGCTGGGTCAGCAACTGAATTCCAGTTTAGATGTGGATTTGGTTGTGGATATGCTCAGCC
ACCTCAG

Alignment

ORF - retro_amel_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPK-HPELADKNVPNL-HVMKAMQSLKSRGYVKEQFAWRHFY
          ML....N...IYELLF.EGVMVAKKDVHMP..H..LAD.N.PNL.HV.KA.QSLKS.GYVKE..A.RHFY
Retrocopy MLKTQMNPTVIYELLFEEGVMVAKKDVHMPN<HLDLADRNIPNL>HVFKATQSLKS*GYVKEYIA*RHFY

Parental  WYLTNEGIQYLRDYLHLPPE-IVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDAYRRSAVPPGAD
          W.LTNEGIQYL.DYLH.PP..IVPA.L..S..ET.RP..KGL.GE.P.R.T.GEA.R..Y.....P.G..
Retrocopy WNLTNEGIQYLCDYLHPPPG<IVPAILHHSSLETERPQSKGLKGEPPTRHT-GEANRNTY-KVLCPLGLT

Parental  KK-AEAGAGSATEFQFRGGFGRGRGQPPQ
          .K.AE.GAGSATEFQFR.GFG.G..QPPQ
Retrocopy RK<AEVGAGSATEFQFRCGFGCGYAQPPQ

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_1706 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1706 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,