RetrogeneDB ID: retro_apla_13

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB744631.1:105826..106100(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5B
• Ensembl ID: ENSAPLG00000007518
• Aliases: None
• Description: cytochrome b5 type B (outer mitochondrial membrane) [Source:HGNC Symbol;Acc:24374]

Sequence

>retro_apla_13
GAACACCCAGGTAGAAAAGAGGTTTTATTGAACAAGCTCACAGAAATGTCACAGAGCTTGGAAGATGTTGGGGTTTCCAC
AGATGCCAGGGAAATCTGAACCAGTACTCCACAGGGGAGGATCCATGTGATAGTAAAAAAACAAGGTTCTAAGGATCAAA
ATACGACATCCTCAAGCTAAGCAGGTTTCTGGTCAACTCCCATGCTGATCCATCTTTGGACCAGTGCTCATAGGTCTAAC
ATGTCACTACTACATGCTGGATGGCAGATCGTCT

Alignment

ORF - retro_apla_13 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.53 %
• Parental protein coverage: 96.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QHPGGEEVLLEQAGKDATESFEDVGHSTDAREM-LKQYYIGE-VHPVRPRGVGQDQNVTSSGQASFWSTW
          .HPG..EVLL.........S.EDVG.STDARE..L.QY..GE..H.........DQN.TSS..A.FWST.
Retrocopy EHPGRKEVLLNKL-TEMSQSLEDVGVSTDAREI<LNQYSTGE>IHVIVKKQGSKDQNTTSSS*AGFWSTP

Parental  LI-PIFGALVLGLMYRYYMLEGRSS
          ....IFG....GL...YYML.GRSS
Retrocopy ML>SIFGPVLIGLTCHYYMLDGRSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Anas platyrhynchos was not studied using RNA-Seq expression data.

ChIP-Seq

Anas platyrhynchos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_apla_13 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_13 was not experimentally validated.

Homology

Retrocopy orthology:

Anas platyrhynchos 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 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13 ,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117,
Dasypus novemcinctus	ENSDNOG00000008313	9 retrocopies	retro_dnov_1424, retro_dnov_2077, retro_dnov_2123, retro_dnov_2310, retro_dnov_2684, retro_dnov_2685, retro_dnov_706, retro_dnov_716, retro_dnov_728,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Homo sapiens	ENSG00000103018	1 retrocopy	retro_hsap_1493,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Gorilla gorilla	ENSGGOG00000015031	1 retrocopy	retro_ggor_1146,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289,
Nomascus leucogenys	ENSNLEG00000005515	1 retrocopy	retro_nleu_1715,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pongo abelii	ENSPPYG00000007506	1 retrocopy	retro_pabe_1243,
Pan troglodytes	ENSPTRG00000008282	1 retrocopy	retro_ptro_1012,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296,
Tarsius syrichta	ENSTSYG00000014292	1 retrocopy	retro_tsyr_2171,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,