RetrogeneDB ID: retro_amel_543

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192494.1:430425..430924(+)
• Located in intron of: ENSAMEG00000003759

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSAMEG00000006003
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_amel_543
TTTCATCAATTTCAAGACAGTACCATTGTGGCTGCTTTTGTAACCCAAGCTGTCTATCATGATACACAACAGTGAAATCT
GAAATATGCAATACAGCGGATCAAGAATGGTACTAGAGCCTAGCACCAATGTACTACAGAGGAGGACAGGCAGCCAGAGT
TGAATATGAGAGCTCAAATCAGGAGTCCTTTGCAAGAGCAGAAAACTGGGTTAAAGAACCTCAGAGGCAAGCAAGTCCTA
ACATTTTCATAGCTTTACCAGAAAACAAAGCTGACCTAGAATAAAAGAGCTGTAGATTTCCAGGAAACACAGTCCTATGC
AGATGACAAAGTTTATTATTCATGGAGACATCAGCCAAAACATCAGTGAATGTAAATGAAATATTTACAGTAATTGCTAA
AAATTTGCCAAATAAGGAACCACAGAATCCAGGAGCAAATTCTGCCAGCGAAGAGTAGCAGAATTTACTGAACCCACACA
GCCAACCAGGGGTCGGTGT

Alignment

ORF - retro_amel_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.47 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FHEYQESTIGAAFLTQTVCLDD-TTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKN
          FH..Q.STI.AAF.TQ.V..D..TTVK.EI..TA.QE.Y.SLAPMYYRG.QAA.V.Y...N...FARA.N
Retrocopy FHQFQDSTIVAAFVTQAVYHDT<TTVKSEICNTADQEWY*SLAPMYYRGGQAARVEYESSNQESFARAEN

Parental  WVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLPK
          WVKE.QRQASPNI.IAL..NKADL..K....F..........SLLFMETSAKT..NVNEIF..IAK.LP.
Retrocopy WVKEPQRQASPNIFIALPENKADLE*K-SCRFPGNTVLCR*QSLLFMETSAKTSVNVNEIFTVIAKNLPN

Parental  NEPQNAAGAPS-RNRGVDLQENNPASRSQC
          .EPQN.........R.....E.....R..C
Retrocopy KEPQNPGANSA<QRRVAEFTEPTQPTRGRC

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_543 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_543 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543 ,
Ailuropoda melanoleuca	ENSAMEG00000012646	1 retrocopy	retro_amel_617,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,