RetrogeneDB ID: retro_apla_4

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB742921.1:474614..475154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAPLG00000001640
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSAPLG00000004509
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_apla_4
ATGGGCAAGGTGCTGTCCAAGATCTTCGGCAACAAGGAGATGCGGATCCTGATGCTGGGGCTGGACGCGGCCGGCAAGAC
CACCATCCTGTACAANATCCTGTACAAACTGAAGCTGGGCCAGTCGGTCACCACCATCCCCACCGTGGGTTTCAACGTGG
AGACGGTCACGTACAAAAACGTCAAGTTCAACGTGTGGGACGTCGGCGGCCAGGATAAGATCCGGCCGCTCTGGAGGCAC
TACTACACGGGCACGCAGGGGTTGATCTTCGTGGTGGACTGCGCCGATCGCGACCGCATCGACGAGGCCCGCCAGGAGCT
GCACCGCATCATCAACGACAGGGAGATGCGGGACGCCATCATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCA
TGAAACCCCACGAAATCCAGGAGAAACTGGGCCTGACCCGGATCAGGGATAGGAATTGGTACGTGCAGCCCTCCTGTGCT
ACTACAGGGGACGGACTCTACGAAGGGCTGACATGGTTAACGTCCAATTATAAATCCTAA

Alignment

ORF - retro_apla_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 87.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFGKKEMRILMVGLDAAGKTT----ILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPL
          .FG.KEMRILM.GLDAAGKTT....ILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIRPL
Retrocopy IFGNKEMRILMLGLDAAGKTTILYXILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPL

Parental  WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHS
          WRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL..
Retrocopy WRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTR

Parental  LRHRNWYIQATCATSGDGLYEGLDWLSNQLRN
          .R.RNWY.Q..CAT.GDGLYEGL.WL......
Retrocopy IRDRNWYVQPSCATTGDGLYEGLTWLTSNYKS

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_4 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_4 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.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4 ,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,