RetrogeneDB ID: retro_amel_394

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192419.1:1455348..1455587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE4
• Ensembl ID: ENSAMEG00000017073
• Aliases: None
• Description: polymerase (DNA-directed), epsilon 4, accessory subunit [Source:HGNC Symbol;Acc:18755]

Sequence

>retro_amel_394
ACGAGTGCACCTCGGCTGGTAGCTGTAGGCTGCCTCTGGTGAGAGTGAAGGCCTTGGTGGAGGTGGATCCCAACATGGTC
CTCAAGAGGCAGAAAGCCATCTTCATTCTGGCACAAGCCTTGGAGATCATTGCAAAAGATGCCTACTACTGCGCTCAACA
AGGGAGAAGGAAAACCCTCCAGAGGAGAGATTCAGATAATGCAATAGAACCTGTGGATAAATCTCCTTTTCTGGAAGGA

Alignment

ORF - retro_amel_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSAP-GARLSRLPLARVKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAYCCAQQGKRKTLQRRDL
          TSAP..A...RLPL.RVKALV..DP...L..Q.AIFILA.A.....E.IAKDAY.CAQQG.RKTLQRRD.
Retrocopy TSAP<SAGSCRLPLVRVKALVEVDPNMVLKRQKAIFILAQA----LEIIAKDAYYCAQQGRRKTLQRRDS

Parental  DNAIEAVDEFAFLEG
          DNAIE.VD...FLEG
Retrocopy DNAIEPVDKSPFLEG

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_394 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_394 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017073	1 retrocopy	retro_amel_394 ,
Callithrix jacchus	ENSCJAG00000017156	1 retrocopy	retro_cjac_1087,
Cavia porcellus	ENSCPOG00000027003	1 retrocopy	retro_cpor_1102,
Felis catus	ENSFCAG00000005983	1 retrocopy	retro_fcat_790,
Homo sapiens	ENSG00000115350	1 retrocopy	retro_hsap_2765,
Gorilla gorilla	ENSGGOG00000004491	1 retrocopy	retro_ggor_1924,
Mustela putorius furo	ENSMPUG00000008356	1 retrocopy	retro_mputfur_305,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,