RetrogeneDB ID: retro_amel_104

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194220.1:38478..39525(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018811
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000009557
• Aliases: None
• Description: None

Sequence

>retro_amel_104
TTCACCATGGAGGACTCAGGAAAGACTTTCGGCTCTGAGGAGGAAGAAGCTAACTACTGGAAAGATCTGGCTATGACCTA
CAAGCAGAGGGCAGAGAATACGCAGGAGGAGCTCCGAGAATTCCAGGAGGGAAGCCGCGAATACGAAGCTGAATTGGAGA
CACAGCTGCAACAGATCGAAACCAGGAACAGGGACCTCCTGTCGGAAAATAACCGCCTTCGCTTGGAGCTGGAAACCATC
AAGGAGAAGTTTGAAACACAGCACTCGGAAGGCTACCGGCAGATCTCGGCCTTGGAGGATGACCTTGCCCAGACCAAAGC
AATTAAGGATCAACTGCAGAAGTACATCCGAGAGCTGGAGCAAGCAAACAATGACTTGGAAAGAGCAAAACAGGCCACAA
TTATGTCTCTGGAAGATTTTGAGCAGCGTTTGAATCAAGCCATTGAAAGAAATGCCTTCCTGGAGAGCGAACTGGATGAG
AAGGAGAATCTCCTAGAATCTGTTCAGCAGCTGAAGGATGAAGCCAGAGATTTGCGGCAGGAGTTGGCTGTGCAGCAGAA
GCAGGAAAAGCCCAGGACCCCCATGCCCAGCTCGGTGGAGGCTGAAAGGACAGATACAGGAGTGCAGGCCACTGGGTCCG
TGCCATCCACACCCATAGCTCATCGGGGACCCAGCGCTAACTTAAACACACCAGGGACGTTCAGACGTGGTCTGGACGAC
TCCACGGGTGGGACCCCCCTCACTCCTGCAGCGCGGATATTGGCCCTCAACATCGTGGGAGACCTGCTTCGGAAAGTAGG
GGCCCTGGAGTCCAAACTTGCATCCTGCGGGAACTTCGTGTATGATCAGTCCCCAAACCGTACGAGTGGCCCCGGCTCGG
GGCGGGGAAGCAAGCACAGAGATGGCGGTGAGAGACAGCCAAGCAGCGCTGGCTTGCCTCTGGGTGACAAAGGGTTGGGA
AAACGCCTGGAATTTGGGAAGCCGCCTTCGAATATTTCCGCACCGTCGCTGCCATCAGCCCAGGGCGTAGTCAAGATGTT
GCTTTAG

Alignment

ORF - retro_amel_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDSGKTFGSEEEEANYWKDLAMTYKQRAENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNR
          MEDSGKTFGSEEEEANYWKDLAMTYKQRAENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNR
Retrocopy MEDSGKTFGSEEEEANYWKDLAMTYKQRAENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNR

Parental  LRLELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQANDDLERAKRRATIMSLEDFE
          LRLELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQAN.DLERAK..ATIMSLEDFE
Retrocopy LRLELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQANNDLERAK-QATIMSLEDFE

Parental  QRLNQAIERNAFLESELDEKENLLESVQRLKDEARDLRQELAVQQKQEKPRTPMPSSVEAERTDTGVQAT
          QRLNQAIERNAFLESELDEKENLLESVQ.LKDEARDLRQELAVQQKQEKPRTPMPSSVEAERTDTGVQAT
Retrocopy QRLNQAIERNAFLESELDEKENLLESVQQLKDEARDLRQELAVQQKQEKPRTPMPSSVEAERTDTGVQAT

Parental  GSVPSTPIAHRGPSANLNTPGTFRRAHPGLDDSTGGTPLTPAARISALNIVGDLLRKVGALESKLASCGN
          GSVPSTPIAHRGPSANLNTPGTFRR...GLDDSTGGTPLTPAARI.ALNIVGDLLRKVGALESKLASCGN
Retrocopy GSVPSTPIAHRGPSANLNTPGTFRR---GLDDSTGGTPLTPAARILALNIVGDLLRKVGALESKLASCGN

Parental  FVYDQSPNRTSGPGSGRGSKHRDGGERQPSSAGLPLGDKGLGKRLEFGKPPSNISAPSLPSAQGVVKMLL
          FVYDQSPNRTSGPGSGRGSKHRDGGERQPSSAGLPLGDKGLGKRLEFGKPPSNISAPSLPSAQGVVKMLL
Retrocopy FVYDQSPNRTSGPGSGRGSKHRDGGERQPSSAGLPLGDKGLGKRLEFGKPPSNISAPSLPSAQGVVKMLL

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_104 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_104 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104 ,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468,