RetrogeneDB ID: retro_amel_378

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192411.1:3156214..3156745(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000012562
• Aliases: None
• Description: None

Sequence

>retro_amel_378
ATGGATGAACTTCAGGACGTTCAACTTGCAGAGATTAAGCCACTTCTAAATGGTAAGACTGGTACACAAAACTTCCAGGA
CTTTGACTACCAGGAACATGACGTAGAAACAACTCATAGTATCATTCACGTCGCCATAAGAGTCCTACCAAAGGGAAACA
GACCAGTTACTCTGACCTATCATGACAGTGGCCTCAATCATAAATCCTGTTTCAATGCGGTCTTTAACTTTGAGGATATG
CAAGAGATCACCCAGCACTTTGCTGTCATGTGGATGCCCCAGGCAGACAGGAAGGTGCACCCTCCTTCCCTACAGGGTAC
CAGTACTCCACAATGGGTGAATTGGCCAAAATGCTGCCTCCTGTTCTTACCCACTTAAGTCTGAAAAGCGTCCCTGGGAT
TGTAGTTGGAGCTGGCGCTTATATCCTCAGCAGATTTGCATTCAATCATCCAGTGCTTGTAGAAGGCCTGTGCTCACAAA
CCTTGACCCTTGTGCTAAAGCTGGATTGACTGGGCAGCTTCCAAAGTAAGC

Alignment

ORF - retro_amel_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDELQDVQLTEIKPLLNDKTGTRNFQDFDCQEHDIETTHGVVHVTIRGLPKGNRPVILTYHDIGLNHKSC
          MDELQDVQL.EIKPLLN.KTGT.NFQDFD.QEHD.ETTH...HV.IR.LPKGNRPV.LTYHD.GLNHKSC
Retrocopy MDELQDVQLAEIKPLLNGKTGTQNFQDFDYQEHDVETTHSIIHVAIRVLPKGNRPVTLTYHDSGLNHKSC

Parental  FNAFFNFEDMQEITQHFAVCHVDAPGQQEGAPSFPTGYQYP-TMDELAEMLPPVLTHLSLKSIIGIGVGA
          FNA.FNFEDMQEITQHFAV............PS...G...P.TM.ELA.MLPPVLTHLSLKS..GI.VGA
Retrocopy FNAVFNFEDMQEITQHFAVMWMPQADRKVHPPSL-QGTSTP<TMGELAKMLPPVLTHLSLKSVPGIVVGA

Parental  GAYILSRFALNHPELVEGL-VLINVDPCAK-GWIDWAASKVS
          GAYILSRFA.NHP.LVEGL.VL.N.DPCAK..WIDWAASKVS
Retrocopy GAYILSRFAFNHPVLVEGL<VLTNLDPCAK<SWIDWAASKVS

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_378 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_378 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012562	1 retrocopy	retro_amel_378 ,
Echinops telfairi	ENSETEG00000002250	1 retrocopy	retro_etel_2102,
Myotis lucifugus	ENSMLUG00000009735	1 retrocopy	retro_mluc_1054,
Otolemur garnettii	ENSOGAG00000000895	1 retrocopy	retro_ogar_515,
Sus scrofa	ENSSSCG00000007322	5 retrocopies	retro_sscr_1116, retro_sscr_144, retro_sscr_519, retro_sscr_539, retro_sscr_937,
Ictidomys tridecemlineatus	ENSSTOG00000022531	1 retrocopy	retro_itri_1284,