RetrogeneDB ID: retro_amel_54

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192462.1:1368320..1368872(+)
• Located in intron of: ENSAMEG00000007425

Retrocopy information

• Ensembl ID: ENSAMEG00000019501
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CBX1
• Ensembl ID: ENSAMEG00000004890
• Aliases: None
• Description: chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]

Sequence

>retro_amel_54
ATGGCCTCCAATAAAACTACATTGCAAAAAATGGGAAAGAAACAGAATGGAAAGAGTAAAAAAGCAGAAGAGGCAGAGCC
TGAAGAATTTGTGGTGGAAAAAGTACTGGACCGACGTGTAGTGAATGGGAAGGTGGAGTATTTCCTGAAGTGGAAGGGAT
TCACAGATGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAA
AAAGCTGGTAAAGAAAAAGATGGTACAAAAAGAAAATCTTTATCTGACAGTGAATCTGATGATAGCAAATCAAAGAAGAA
AAGAGATGCTGCTGATAAACCAAGAGGCTTTGCCAGAGGTCTTGATCCTGAACGAATAATTGGTGCCACAGACAGCAGTG
GAGAATTAATGTTTCTCATGAAATGGAAAGATTCAGATGAGGAAGACTTGGTGCTGGCAAAAGAGGCAAATATGAAGTGT
CCTCAAATTGTAATTGCTTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAATAA

Alignment

ORF - retro_amel_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 95.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAKFLQS
          MGKKQN.K......E.E.EE.VVEKVLDRRVV.GKVEY.LKWKGF.D.DNTWEPEENLDCP.LI..FL.S
Retrocopy MGKKQNGKS-KKAEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNS

Parental  QKTAHETDKSEGGKRKADSDSEDKGEESKPKKKKEEVRGESEKPRGFARGLEPERIIGATDSSGELMFLM
          QK...E.D...G.KRK..SDSE.....SK.KKK....R....KPRGFARGL.PERIIGATDSSGELMFLM
Retrocopy QKAGKEKD---GTKRKSLSDSES--DDSKSKKK----RDAADKPRGFARGLDPERIIGATDSSGELMFLM

Parental  KWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSED
          KWK.SDE.DLV.AKEAN.KCPQ.VI.FYEERLTWHS.P...
Retrocopy KWKDSDEEDLVLAKEANMKCPQIVIAFYEERLTWHSCPEDE

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_54 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_54 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 28 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004890	2 retrocopies	retro_amel_1228, retro_amel_54 ,
Ailuropoda melanoleuca	ENSAMEG00000005969	1 retrocopy	retro_amel_1184,
Bos taurus	ENSBTAG00000002949	9 retrocopies	retro_btau_1121, retro_btau_1394, retro_btau_148, retro_btau_1583, retro_btau_1615, retro_btau_550, retro_btau_558, retro_btau_714, retro_btau_807,
Canis familiaris	ENSCAFG00000016832	1 retrocopy	retro_cfam_804,
Choloepus hoffmanni	ENSCHOG00000011957	2 retrocopies	retro_chof_1860, retro_chof_2185,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Dipodomys ordii	ENSDORG00000000716	2 retrocopies	retro_dord_594, retro_dord_709,
Erinaceus europaeus	ENSEEUG00000004874	3 retrocopies	retro_eeur_121, retro_eeur_228, retro_eeur_396,
Echinops telfairi	ENSETEG00000000203	7 retrocopies	retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Homo sapiens	ENSG00000108468	3 retrocopies	retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Gorilla gorilla	ENSGGOG00000024063	3 retrocopies	retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Microcebus murinus	ENSMICG00000009510	4 retrocopies	retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Myotis lucifugus	ENSMLUG00000005030	2 retrocopies	retro_mluc_1000, retro_mluc_1533,
Mustela putorius furo	ENSMPUG00000015302	1 retrocopy	retro_mputfur_1457,
Mus musculus	ENSMUSG00000018666	1 retrocopy	retro_mmus_3108,
Nomascus leucogenys	ENSNLEG00000002435	4 retrocopies	retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Oryctolagus cuniculus	ENSOCUG00000008021	3 retrocopies	retro_ocun_177, retro_ocun_442, retro_ocun_55,
Otolemur garnettii	ENSOGAG00000005658	9 retrocopies	retro_ogar_1087, retro_ogar_1092, retro_ogar_1322, retro_ogar_2056, retro_ogar_2396, retro_ogar_2443, retro_ogar_2840, retro_ogar_2880, retro_ogar_368,
Ochotona princeps	ENSOPRG00000003699	1 retrocopy	retro_opri_552,
Procavia capensis	ENSPCAG00000002381	2 retrocopies	retro_pcap_134, retro_pcap_308,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Rattus norvegicus	ENSRNOG00000008689	2 retrocopies	retro_rnor_2388, retro_rnor_2841,
Sarcophilus harrisii	ENSSHAG00000008192	1 retrocopy	retro_shar_76,
Sus scrofa	ENSSSCG00000017529	1 retrocopy	retro_sscr_635,
Ictidomys tridecemlineatus	ENSSTOG00000023986	3 retrocopies	retro_itri_1282, retro_itri_1599, retro_itri_1867,
Tupaia belangeri	ENSTBEG00000014931	39 retrocopies	retro_tbel_1388, retro_tbel_1557, retro_tbel_1613, retro_tbel_1655, retro_tbel_1663, retro_tbel_1794, retro_tbel_2124, retro_tbel_2130, retro_tbel_2281, retro_tbel_2313, retro_tbel_2346, retro_tbel_2539, retro_tbel_2559, retro_tbel_2571, retro_tbel_2587, retro_tbel_270, retro_tbel_2713, retro_tbel_2716, retro_tbel_2752, retro_tbel_2809, retro_tbel_2835, retro_tbel_2854, retro_tbel_2926, retro_tbel_2993, retro_tbel_303, retro_tbel_3236, retro_tbel_3370, retro_tbel_3685, retro_tbel_3998, retro_tbel_4032, retro_tbel_4202, retro_tbel_4611, retro_tbel_4630, retro_tbel_484, retro_tbel_558, retro_tbel_687, retro_tbel_792, retro_tbel_793, retro_tbel_938,
Tarsius syrichta	ENSTSYG00000004769	2 retrocopies	retro_tsyr_1672, retro_tsyr_467,