RetrogeneDB ID: retro_sscr_429

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:26854760..26855300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSSSCG00000013992
• Aliases: None
• Description: Sus scrofa ADP-ribosylation factor 1 (ARF1), mRNA. [Source:RefSeq mRNA;Acc:NM_001160427]

Sequence

>retro_sscr_429
GGGATCATCTTTGCAAACCTCTTCAAGAGCCTTTTTGGGAAGACGGAAATGCGTATTCTCATGGTGGGTCTAGATGCTGC
AGGAAAGACCACCATCCTGTACAAACTGAAGCTGGGGGAAAACGTGACCACCATTCCTGCTCCAGGCTTCAACGTGGAGA
CTGTGGAGCATGAGAGTATCAGCTTCACCGTGTGGGTCGAGGGCGGCCAGGACAAGATCCGGCCACTGTGACGCCACTCC
TTCCAGCACATGCAATGTCTCATCTTTGCAGTTAATGGTAATGACAGAGAGCGTGTGAAGGAGGCCCGAGAGGAGCTCAT
GAGGATGCTGGCAGACGACGAGCTCAGAGACGCTGTTCTGCTCATGTTTGCTAACAAACAGAAGTGCCCCGATGCCATGA
ATGCAGCTGAGATCACTGACAAGCTGGGCCTACACTCTCTGCGCCACAGGAACTGGTACCTCCAGTCCACCTGTGCCACC
AGTGGTGATAGGCTCTATGAGGGACTGGACTGGCTGTGCCATCAGCTCCGGAACCAGAAG

Alignment

ORF - retro_sscr_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQ
          G.IFANLFK.LFGK.EMRILMVGLDAAGKTTILYKLKLGE.VTTIP..GFNVETVE...ISFTVW..GGQ
Retrocopy GIIFANLFKSLFGKTEMRILMVGLDAAGKTTILYKLKLGENVTTIPAPGFNVETVEHESISFTVWVEGGQ

Parental  DKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITD
          DKIRPL.RH.FQ..Q.LIF.V..NDRERV.EAREELMRMLA.DELRDAVLL.FANKQ..P.AMNAAEITD
Retrocopy DKIRPL*RHSFQHMQCLIFAVNGNDRERVKEAREELMRMLADDELRDAVLLMFANKQKCPDAMNAAEITD

Parental  KLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          KLGLHSLRHRNWY.Q.TCATSGD.LYEGLDWL..QLRNQK
Retrocopy KLGLHSLRHRNWYLQSTCATSGDRLYEGLDWLCHQLRNQK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	490.71 RPM
SRP014902_testis	0.00 RPM	303.54 RPM
SRP018288_heart	0.00 RPM	228.17 RPM
SRP018288_kidney	0.00 RPM	448.10 RPM
SRP018288_liver	0.00 RPM	281.60 RPM
SRP018288_lung	0.00 RPM	356.60 RPM
SRP018856_adipose	0.06 RPM	438.98 RPM
SRP035408_brain	0.06 RPM	255.16 RPM
SRP035408_liver	0.00 RPM	244.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_429 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_429 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 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,
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,
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,