RetrogeneDB ID: retro_amel_1551

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193598.1:294257..294680(-)
• Located in intron of: ENSAMEG00000006647

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM242
• Ensembl ID: ENSAMEG00000009699
• Aliases: None
• Description: transmembrane protein 242 [Source:HGNC Symbol;Acc:17206]

Sequence

>retro_amel_1551
ATGGAGACGGCTAGTGCTTGGCCTGGGCAGTCGTCCTCTTGTATCAAGGCTCCAGGATCCACAGACAATATGCTTTTCCT
TTTGAAAGGTAGAGTTTTCCTTGGTACCATGGCTGCAGCAGGAATTCTAGCCAGATTTGTTACAACATTATCATTGGCTA
AAAAGAAAAGCCCTGAATGGTTCAGTAAAGGAAGCATGGCCACAGCTGCCTTACCAGAGAGCAGGTCTTCCCTTGCCTTG
CGAGCCCTGGGTTGGGGCTCACTTTATGCATGGTGTGGGGTTGGTGTGATCAGCTTCGCAGTCTGGAAAGCTTTAGAAAT
TCACGGTATGAAAGATTTTCAAAGTAAAATGCAATCGATATTTCCAGCAATTCCCCAAAACTCTGAAACATCTCTTGAGT
GGGAGGAAGCATTGAAATCCAAG

Alignment

ORF - retro_amel_1551 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METAGPGSGPSSSRLEAPGSADDPLFLVKGGVFLGTVAAAGMLAGFVTTLSLAKKKSPEWFNKGSMATAA
          META....G.SSS...APGS.D..LFL.KG.VFLGT.AAAG.LA.FVTTLSLAKKKSPEWF.KGSMATAA
Retrocopy METASAWPGQSSSCIKAPGSTDNMLFLLKGRVFLGTMAAAGILARFVTTLSLAKKKSPEWFSKGSMATAA

Parental  LPESGSSLALRALGWGSLYAWCGVGVISFAVWKALGVHSMKDFRSKMQSIFPAIPKNSESSLQWEEALKS
          LPES.SSLALRALGWGSLYAWCGVGVISFAVWKAL..H.MKDF.SKMQSIFPAIP.NSE.SL.WEEALKS
Retrocopy LPESRSSLALRALGWGSLYAWCGVGVISFAVWKALEIHGMKDFQSKMQSIFPAIPQNSETSLEWEEALKS

Parental  K
          K
Retrocopy K

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_1551 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1551 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	ENSAMEG00000009699	1 retrocopy	retro_amel_1551 ,
Cavia porcellus	ENSCPOG00000022213	1 retrocopy	retro_cpor_160,
Equus caballus	ENSECAG00000016335	1 retrocopy	retro_ecab_898,
Homo sapiens	ENSG00000215712	1 retrocopy	retro_hsap_1016,
Macaca mulatta	ENSMMUG00000011814	1 retrocopy	retro_mmul_812,
Nomascus leucogenys	ENSNLEG00000010676	1 retrocopy	retro_nleu_222,
Otolemur garnettii	ENSOGAG00000007646	1 retrocopy	retro_ogar_946,
Pongo abelii	ENSPPYG00000017271	1 retrocopy	retro_pabe_853,
Pan troglodytes	ENSPTRG00000018735	1 retrocopy	retro_ptro_747,