RetrogeneDB ID: retro_amel_885

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192711.1:610987..611548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRAS
• Ensembl ID: ENSAMEG00000017134
• Aliases: None
• Description: neuroblastoma RAS viral (v-ras) oncogene homolog [Source:HGNC Symbol;Acc:7989]

Sequence

>retro_amel_885
GAATACAAACTGGTGGTGGTTGCAGGAAGTGATGTTGAGGAAAGTGCACTGACAAGCCAGCTAATCCAGAACCACTTTGT
AGCTGAATATGATCCCACCACAGAGGATTCTTACTGAAAACAGGTGGTTATAGATGGTGAAACCTGTCTGTTGGACATAC
TGTGTACAGCTGGTCAAGAAGAGTACACTGCCATGAGAGAGCAGCACCTGAGGACAGGTAAAGGCTTCCTCTGTGTATCT
GCCATCACTAATAGCAAATCATTTGCAGTCATTAACTTCTACAGGGGACAGATTAAGCAAGTAAAAGACTCAGGGGGTGT
ACCTATGATGCTAGTAGGAAACAAGTGTGATTTGTCAACAAGAACAGTTGACACAAAACAAGCCCACCAACTGGCCAAGA
GTTATGGGGTTCTATTCACTGAAACCTCAGCCAAGACCAGAAGATTGTCGAAGATGCCTTTTACACATTGGTAAGAGGTG
TTTTTTAAGTATCAAATGAAGAAACTCAACAGCAATAATGATGGGACTCAAGGTTGAATGGGGTTACCATGCATAGTGAT
G

Alignment

ORF - retro_amel_885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 96.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYM
          EYKLVVV....V..SALT.QLIQNHFV.EYDPT.EDSY.KQVVIDGETCLLDIL.TAGQEEY.AMR.Q..
Retrocopy EYKLVVVAGSDVEESALTSQLIQNHFVAEYDPTTEDSY*KQVVIDGETCLLDILCTAGQEEYTAMREQHL

Parental  RTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIPFI
          RTG.GFLCV.AI.NSKSFA.IN.YR.QIK.VKDS..VPM.LVGNKCDL.TRTVDTKQAH.LAKSYG..F.
Retrocopy RTGKGFLCVSAITNSKSFAVINFYRGQIKQVKDSGGVPMMLVGNKCDLSTRTVDTKQAHQLAKSYGVLFT

Parental  ETSAKTR-QGVEDAFYTLVREI-RQYRMKKLNSSDDGTQGCMGLPCVVI
          ETSAKTR...VEDAFYTLVR.....Y.MKKLNS..DGTQG.MGLPC.V.
Retrocopy ETSAKTR<KIVEDAFYTLVRGV>FKYQMKKLNSNNDGTQG*MGLPCIVM

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_885 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_885 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885 ,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,