RetrogeneDB ID: retro_amel_1421

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193352.1:699351..699594(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000016604
• Aliases: None
• Description: None

Sequence

>retro_amel_1421
GAAATCGAGAAAATCGTTTGGGAAAATACTTCAGACGTTATATTGGTTGGTCTCCGGGATGACCAAGACAATAAAGCCGA
TGTAACTTTAAAATACAATGCAGACGAAGCTGGAAGTCTGAGGGCATATGGCGAGCTTCCAGAGCGTTTTAGAATCATTG
AAACTGATACATTCGGTCTTGGAGATGAATTTTGATTCAGTTTGATGTCGTCGATTGGGGATGATGATGAAGACATCAGT
GAT

Alignment

ORF - retro_amel_1421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQ-FD
          ...K.VW.NTSD.ILVGLRD.QDNKADV.LKYNADEA.SL.AYGELPE...I.ETDTFG.GD........
Retrocopy EIEKIVWENTSDVILVGLRDDQDNKADVTLKYNADEAGSLRAYGELPERFRIIETDTFGLGDEF*FSLMS

Parental  DIGDDDEDIDD
          .IGDDDEDI.D
Retrocopy SIGDDDEDISD

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_1421 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1421 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421 ,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,