RetrogeneDB ID: retro_amel_121

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193550.1:540597..541059(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019431
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSAMEG00000004684
• Aliases: None
• Description: None

Sequence

>retro_amel_121
ATGGCACCAAAGGCAAAGAAGGAAAACCCTGACCCACCCAAAGCAGAAGCCAAAGCAAAGGCTTTGAAGGCCAAGAAAGC
GGTGCTGAATAGGCGTCCACAGTCACAAAGAAAAAAGATCCGCATGTCACCTACATTCCCACGGCCCAAGACACTGTGTC
TCCGAAGGCAGCCCAAATATCCTCCAAAGAGTGCCCCCAGGAGAAACAAGGTTAACCACAATGCCATCATCAAGTTCCCC
CTGACTATGGAGTCAGTCATGAAAATAGAAGACAACACACTTGTGTTCATTATGGATGTCAAGGCCAACAAGCACCAGAT
CAAACAGGCCGTGAAGAAGCTCTATGACATTGACGGGGCCAAGGTCAACACCCTGATCAGGCCCAATGGAGAGAAGAAGG
CATACGTTCAACTGGCTCCTGACTATGATGCTTTGGATGTTGCCAACAAAATTGGGACCTAA

Alignment

ORF - retro_amel_121 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 98.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKPKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNK
          MAPK.KKE.P.PPKAEAKAKALKAKKAVL........KKIR.SPTF.RPKTL.LRRQPKYP.KSAPRRNK
Retrocopy MAPKAKKENPDPPKAEAKAKALKAKKAVLNRRPQSQRKKIRMSPTFPRPKTLCLRRQPKYPPKSAPRRNK

Parental  LDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
          ..H.AIIKFPLT.ES.M.KIED.NTLVFI.DVKANKHQIKQAVKKLYDID.AKVNTLIRP.GEKKAYV.L
Retrocopy VNHNAIIKFPLTMESVM-KIED-NTLVFIMDVKANKHQIKQAVKKLYDIDGAKVNTLIRPNGEKKAYVQL

Parental  APDYDALDVANKIG
          APDYDALDVANKIG
Retrocopy APDYDALDVANKIG

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_121 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_121 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 10 parental genes, and 278 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005311	2 retrocopies	retro_acar_152, retro_acar_173,
Ailuropoda melanoleuca	ENSAMEG00000004684	31 retrocopies	retro_amel_1044, retro_amel_1154, retro_amel_121 , retro_amel_1254, retro_amel_1302, retro_amel_1383, retro_amel_1391, retro_amel_1423, retro_amel_1503, retro_amel_1505, retro_amel_1511, retro_amel_1527, retro_amel_1532, retro_amel_1568, retro_amel_1576, retro_amel_1585, retro_amel_1702, retro_amel_1822, retro_amel_288, retro_amel_304, retro_amel_323, retro_amel_467, retro_amel_479, retro_amel_514, retro_amel_667, retro_amel_75, retro_amel_773, retro_amel_843,