RetrogeneDB ID: retro_amel_672

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192563.1:1795661..1795998(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000013041
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NOL12
• Ensembl ID: ENSAMEG00000010139
• Aliases: None
• Description: nucleolar protein 12 [Source:HGNC Symbol;Acc:28585]

Sequence

>retro_amel_672
AAAGGGCAGCAAGATGGTGATGACCAGGGGCCTCTGCTCATTCTCAGCTTCAGGGAGAAGCAGACGGAGTACCCGACAGG
TGTTCGCAAGCGGAAGCTGGAGCCGAAGAAGGAGGCCGTTATCCTTCATGCCGCAACAGTTCAAGGGGCGCAAGCTCTGG
GAGGAGCGCCCCCGGGAATCCTTGAAGATGCTGGCGGAGAGAGAGGAGGCTCTGGAAGAGTCACATGAGCTGCAGTGGCT
GGTGACCCCGAAGACAGAGTTGGCGCAGTGTGACCACCCCAACCACACAGCCACTGTGAGCGCCACCAGCAACTGGTACC
TCTCCGGGACCTGCCTG

Alignment

ORF - retro_amel_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.31 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVE-RKKAAIEEIKHRLKEEQKKLREERHQEYLKMLAE
          K...DGDD..P.L.LSF..EK..EY.TG..KRK.E.R............K....KL.EER..E.LKMLAE
Retrocopy KGQQDGDDQGPLLILSF-REKQTEYPTGVRKRKLE>RRRRPLSFMPQQFKG--RKLWEERPRESLKMLAE

Parental  REEALEEADELDRLVTAKTESVQYDHPNHTVTVTTISDLDLSGARL
          REEALEE..EL..LVT.KTE..Q.DHPNHT.TV...S...LSG..L
Retrocopy REEALEESHELQWLVTPKTELAQCDHPNHTATVSATSNWYLSGTCL

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_672 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_672 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010139	1 retrocopy	retro_amel_672 ,
Callithrix jacchus	ENSCJAG00000012487	1 retrocopy	retro_cjac_538,
Equus caballus	ENSECAG00000011050	1 retrocopy	retro_ecab_126,
Felis catus	ENSFCAG00000004273	1 retrocopy	retro_fcat_757,
Oryctolagus cuniculus	ENSOCUG00000017013	1 retrocopy	retro_ocun_1698,
Otolemur garnettii	ENSOGAG00000008255	1 retrocopy	retro_ogar_2914,
Pteropus vampyrus	ENSPVAG00000010097	1 retrocopy	retro_pvam_1022,
Tupaia belangeri	ENSTBEG00000009745	1 retrocopy	retro_tbel_3215,
Tursiops truncatus	ENSTTRG00000004799	1 retrocopy	retro_ttru_1165,