RetrogeneDB ID: retro_sscr_315

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:34739646..34740122(+)
• Located in intron of: ENSSSCG00000011363

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT20
• Ensembl ID: ENSSSCG00000023719
• Aliases: None
• Description: intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]

Sequence

>retro_sscr_315
ATGACACACCTCCTCCTAGCTGCCACTATCAACACTTAAGAGCAGAACTTTTCTAGGGAAGTTGGAAGGGAAAGAGCTAT
TGCCAAGGTCATCCTGAGTGAAGCAGGGTTGTGCTTTGATGAGCTAAACAAGCTGCAGGTATTGGACCCAGAAGCTACTG
AGCAGACCATAGAGCTCAAGGAAGAAGTACAAGGAATTTGTGGACAAAACTGGCCAGTTTCAGAAAATAGTTGGTGGTTC
AATTGGGTTTGTTGACCAACTTGCCAAAGAAGCAGAAAACGAGAAGATGAAGCCCACTGGTGCTTAGAGCTTGCTCAAAT
CTACAGCAAAGCAGAGAGAAGCCCAACAGAAGCAACTCTAGGCACTAGCAGCAGAAAGGAAAATGCAGCTCAAAAAGTTA
TAAGGTTGAATGTGAAGATACATGCAAAGGAGAAGTAGAACAAAATGAACTTATTAACAAATTTATTTTACAGAAA

Alignment

ORF - retro_sscr_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTYLLLAATVTPSEQNFSREAGRETAMAKDILGEAGLHFDELNKLRVLDPEVTQQTIELKEEC-KDFVDK
          MT.LLLAAT....EQNFSRE.GRE.A.AK.IL.EAGL.FDELNKL.VLDPE.T.QTIELKEE..K.FVDK
Retrocopy MTHLLLAATINT*EQNFSREVGRERAIAKVILSEAGLCFDELNKLQVLDPEATEQTIELKEEV>KEFVDK

Parental  IGQFQKIVGGLIELVDQLAKEAENEKMKAIGARNLLKSIAKQREAQQQQLQALIAEKKMQLER-YRVEYE
          .GQFQKIVGG.I..VDQLAKEAENEKMK..GA..LLKS.AKQREAQQ.QL.AL.AE.KMQL...Y.VE.E
Retrocopy TGQFQKIVGGSIGFVDQLAKEAENEKMKPTGA*SLLKSTAKQREAQQKQL*ALAAERKMQLKK>YKVECE

Parental  ALCKVEAEQNEFIDQFIFQK
          ..CK.E.EQNE.I..FI.QK
Retrocopy DTCKGEVEQNELINKFILQK

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	41.15 RPM
SRP014902_testis	0.00 RPM	146.96 RPM
SRP018288_heart	0.03 RPM	14.22 RPM
SRP018288_kidney	0.00 RPM	33.79 RPM
SRP018288_liver	0.00 RPM	102.98 RPM
SRP018288_lung	0.10 RPM	17.11 RPM
SRP018856_adipose	0.00 RPM	27.77 RPM
SRP035408_brain	0.00 RPM	39.89 RPM
SRP035408_liver	0.00 RPM	36.72 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_315 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_315 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005111	2 retrocopies	retro_amel_1011, retro_amel_1337,
Bos taurus	ENSBTAG00000008110	1 retrocopy	retro_btau_257,
Callithrix jacchus	ENSCJAG00000012534	2 retrocopies	retro_cjac_2404, retro_cjac_687,
Cavia porcellus	ENSCPOG00000003153	1 retrocopy	retro_cpor_152,
Echinops telfairi	ENSETEG00000018843	2 retrocopies	retro_etel_1045, retro_etel_1181,
Homo sapiens	ENSG00000109083	1 retrocopy	retro_hsap_1314,
Gorilla gorilla	ENSGGOG00000004568	2 retrocopies	retro_ggor_1026, retro_ggor_1217,
Microcebus murinus	ENSMICG00000005074	1 retrocopy	retro_mmur_987,
Myotis lucifugus	ENSMLUG00000008709	2 retrocopies	retro_mluc_180, retro_mluc_1924,
Macaca mulatta	ENSMMUG00000019143	2 retrocopies	retro_mmul_2165, retro_mmul_2234,
Monodelphis domestica	ENSMODG00000019233	1 retrocopy	retro_mdom_681,
Mustela putorius furo	ENSMPUG00000014353	1 retrocopy	retro_mputfur_247,
Mus musculus	ENSMUSG00000001105	1 retrocopy	retro_mmus_3245,
Nomascus leucogenys	ENSNLEG00000001883	2 retrocopies	retro_nleu_1067, retro_nleu_1941,
Oryctolagus cuniculus	ENSOCUG00000007773	1 retrocopy	retro_ocun_438,
Otolemur garnettii	ENSOGAG00000003333	2 retrocopies	retro_ogar_1169, retro_ogar_72,
Ochotona princeps	ENSOPRG00000005826	6 retrocopies	retro_opri_110, retro_opri_1185, retro_opri_205, retro_opri_293, retro_opri_375, retro_opri_872,
Pongo abelii	ENSPPYG00000008087	2 retrocopies	retro_pabe_1097, retro_pabe_1322,
Pan troglodytes	ENSPTRG00000008911	1 retrocopy	retro_ptro_1079,
Sus scrofa	ENSSSCG00000023719	1 retrocopy	retro_sscr_315 ,
Ictidomys tridecemlineatus	ENSSTOG00000007554	1 retrocopy	retro_itri_713,
Tupaia belangeri	ENSTBEG00000005557	2 retrocopies	retro_tbel_180, retro_tbel_1954,