RetrogeneDB ID: retro_amel_315

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192381.1:889547..889836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSAMEG00000013225
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_amel_315
CAGGAGGCAAAACTGTCAACTGAGGACTTGGGGGTAAGAGGGAAAGAGAATACATTAAACTCAAAGTCATTGGACAGGAT
AGCATTGAGATTTGCTTCTAAGTGAAGATGACAACACATCTCAAGAAACCCAAAGACTTGTGCTGTCAAAGACAGGGAGT
TCCAATGAATTCACTCAGGTTTCTCTTTGAAGGTCAGAGAATTGCTGATAATCACACTGCAAAAGAACTGGGAATGAAGA
AGATGTGATCGAAGTTTATCAGGAACAAACGGGATCATTCAACAATTTA

Alignment

ORF - retro_amel_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEAKPSTEDLG-DKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIA
          QEAK.STEDLG..K.E.EYIKLKVIGQDS.EI.F.VKMTTHLKK.K...CQRQGVPMNSLRFLFEGQRIA
Retrocopy QEAKLSTEDLG<GKREREYIKLKVIGQDSIEICF*VKMTTHLKKPKDLCCQRQGVPMNSLRFLFEGQRIA

Parental  DNHTPKELGM-EEEDVIEVYQEQTGGHSTI
          DNHT.KELGM.EE.DVIEVYQEQTG.....
Retrocopy DNHTAKELGM<EE-DVIEVYQEQTGSFNNL

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_315 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_315 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 15 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002071	3 retrocopies	retro_amel_1388, retro_amel_1586, retro_amel_1863,
Ailuropoda melanoleuca	ENSAMEG00000009189	13 retrocopies	retro_amel_1097, retro_amel_1125, retro_amel_1199, retro_amel_1263, retro_amel_1434, retro_amel_152, retro_amel_1665, retro_amel_276, retro_amel_35, retro_amel_616, retro_amel_653, retro_amel_662, retro_amel_722,
Ailuropoda melanoleuca	ENSAMEG00000013225	5 retrocopies	retro_amel_1068, retro_amel_233, retro_amel_236, retro_amel_315 , retro_amel_49,
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190, retro_chof_2068,
Dasypus novemcinctus	ENSDNOG00000015868	10 retrocopies	retro_dnov_1070, retro_dnov_1324, retro_dnov_1610, retro_dnov_1623, retro_dnov_1826, retro_dnov_1876, retro_dnov_2068, retro_dnov_2330, retro_dnov_2423, retro_dnov_997,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,