RetrogeneDB ID: retro_amel_1168

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192988.1:987186..987414(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSAMEG00000014744
• Aliases: None
• Description: signal recognition particle 9kDa [Source:HGNC Symbol;Acc:11304]

Sequence

>retro_amel_1168
TCAGCAGCGCCGCTGAGAAACCACCTCACCAGCCCTATGAAGGCACGTGGGGTTCCCCAAAACTGGCATTCTGAAGGGAA
TTCGTGTATTAAAGTAACAGGTGAGTTAGTTTGTTTGGTGCAAAGAACAGACCAAACCTGAGTCCTAAAGAAGATTGAGA
AATTCCACAGTCAACTAAGGCCACTGCTGGTTACCAAGCAGTGCTGCAGTGTTGCCATGGAAACAGAC

Alignment

ORF - retro_amel_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 88.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRAAEKLYLADPMKARVVLKYRHSDGSLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLMRLMVAKESRS
          S.A.....L..PMKAR.V....HS.G..CIKVT..LVCLV.RTDQ....KKIEKFHSQL..L.V.K...S
Retrocopy SAAPLRNHLTSPMKARGVPQNWHSEGNSCIKVTGELVCLVQRTDQT*VLKKIEKFHSQLRPLLVTKQCCS

Parental  VAMETD
          VAMETD
Retrocopy VAMETD

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_1168 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1168 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014744	2 retrocopies	retro_amel_1168 , retro_amel_898,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Homo sapiens	ENSG00000143742	1 retrocopy	retro_hsap_711,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,
Ochotona princeps	ENSOPRG00000012133	2 retrocopies	retro_opri_1135, retro_opri_324,