RetrogeneDB ID: retro_amel_716

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192585.1:408071..408338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2F
• Ensembl ID: ENSAMEG00000010331
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide F [Source:HGNC Symbol;Acc:9193]

Sequence

>retro_amel_716
CTTCCTTTATGGAGAGAACCACAGACCATCCAGAAACGAATCACCACACCATATTTGACCAACTATGAGCGAGCCTGCTT
GCTGGGCACCTGAGCCCTCCAAATAGTGATGCATGCCCCTGGGATGGTGGAGCAGGTGAGGGAAACAGATCCCTTGCTCA
TCACCATGAACGAGCTCAAGGCCTGAAAGATCCCTGTCATCATTCACTACTACCTCCCAGAGGGGAGTTATGAAGACTGG
GGGGTAGACAAGCTCATCATCACCGAC

Alignment

ORF - retro_amel_716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.91 %
• Parental protein coverage: 70.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRR
          LP....PQ..QKRITTPY.T.YERA..LGT.ALQI.M.AP.MVE...ETDPLLI.M.ELKA.KIP.II..
Retrocopy LPLWREPQTIQKRITTPYLTNYERACLLGT*ALQIVMHAPGMVEQVRETDPLLITMNELKA*KIPVIIHY

Parental  YLPDGSYEDWGVDELIITD
          YLP.GSYEDWGVD.LIITD
Retrocopy YLPEGSYEDWGVDKLIITD

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_716 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_716 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010331	1 retrocopy	retro_amel_716 ,
Bos taurus	ENSBTAG00000004820	1 retrocopy	retro_btau_1648,
Canis familiaris	ENSCAFG00000001437	1 retrocopy	retro_cfam_596,
Myotis lucifugus	ENSMLUG00000014315	1 retrocopy	retro_mluc_199,
Monodelphis domestica	ENSMODG00000019063	2 retrocopies	retro_mdom_1276, retro_mdom_2015,
Mustela putorius furo	ENSMPUG00000012997	1 retrocopy	retro_mputfur_1158,
Otolemur garnettii	ENSOGAG00000025463	1 retrocopy	retro_ogar_1639,