RetrogeneDB ID: retro_sscr_1219

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: Y:259088..259576(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000028079
• Aliases: None
• Description: Sus scrofa ribosomal protein L15 (RPL15), mRNA. [Source:RefSeq mRNA;Acc:NM_001244065]

Sequence

>retro_sscr_1219
TCTCCCCGTCCCCAGCCCAATAAGGCATGCAGGCTTGGGTAAAAGGCCAAGCAGGGTTATGTCATGTATCAGATTTGTTT
GCAAGTGGTGGGGTTGCAAATGCCCATTTCCTAAGTGTGACATCTATGGCAAGCATGTCCACTAGGGTGTCAACCATCTA
AAGTTTGTTAAAAACCTTCAATCTGTTGCTGAGGAGTGAGTTGAATGTCCCTTGTGTGGCTCTGAGTGCCCTGAATTGTT
ACTGTGTTGGTGAAGATGCTAAGTACAAATTATTTGAAGTTATCCTCATTGACCCATTCCATAAAGCTATCAGAAGTAAT
TCTGACACTCAGAGGATCACCAAAGCAGTCCACAAGTACAGTGAGATGTGAGGGCTTACTGCTGTAGGCAGAAAGAGCCA
TGGCCTTAGGAAGGGCCACAAGTTCCGTCACACTATTGGTTGTTCTTGCTGTGGGGCTTGGAGAAGGCACAACACTCTTC
AGCTCCAC

Alignment

ORF - retro_sscr_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 79.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  APRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPV-PKGATYGKPVHHGVNQLKFA-RSLQSVAEERA
          .PRP..P.KA.RLG.KAKQGYV.Y.I.....G...P..PK...YGK.VH.GVN.LKF.............
Retrocopy SPRP-QPNKACRLG*KAKQGYVMYQICLQVVGLQMPI>PKCDIYGKHVH*GVNHLKFV>KTFNLLLRSEL

Parental  GRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGK
          ...C.AL..LN.Y.VGED..YK.FEVILIDPFHKAIR.N.DTQ.ITK.VHK..EM.GLT..GRKS.GL.K
Retrocopy NVPCVALSALNCYCVGEDAKYKLFEVILIDPFHKAIRSNSDTQRITKAVHKYSEM*GLTAVGRKSHGLRK

Parental  GHKFHHTIGGSRRAAWRRRNTLQLH
          GHKF.HTIG.S...AWRR.NTLQLH
Retrocopy GHKFRHTIGCSCCGAWRRHNTLQLH

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	0.27 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	4.14 RPM
SRP018288_kidney	0.00 RPM	5.71 RPM
SRP018288_liver	0.00 RPM	2.08 RPM
SRP018288_lung	0.00 RPM	0.51 RPM
SRP018856_adipose	0.00 RPM	2.73 RPM
SRP035408_brain	0.00 RPM	2.79 RPM
SRP035408_liver	0.00 RPM	1.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1219 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 167 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033080	2 retrocopies	retro_btau_152, retro_btau_201,
Canis familiaris	ENSCAFG00000005764	5 retrocopies	retro_cfam_1003, retro_cfam_1159, retro_cfam_1630, retro_cfam_572, retro_cfam_656,
Cavia porcellus	ENSCPOG00000002253	4 retrocopies	retro_cpor_620, retro_cpor_807, retro_cpor_900, retro_cpor_978,
Erinaceus europaeus	ENSEEUG00000011286	5 retrocopies	retro_eeur_200, retro_eeur_28, retro_eeur_400, retro_eeur_685, retro_eeur_694,
Echinops telfairi	ENSETEG00000015044	4 retrocopies	retro_etel_1438, retro_etel_431, retro_etel_658, retro_etel_943,
Felis catus	ENSFCAG00000026237	6 retrocopies	retro_fcat_1820, retro_fcat_285, retro_fcat_306, retro_fcat_610, retro_fcat_930, retro_fcat_985,
Homo sapiens	ENSG00000174748	14 retrocopies	retro_hsap_1294, retro_hsap_1804, retro_hsap_2160, retro_hsap_2870, retro_hsap_2927, retro_hsap_3095, retro_hsap_3422, retro_hsap_3661, retro_hsap_3792, retro_hsap_592, retro_hsap_631, retro_hsap_791, retro_hsap_930, retro_hsap_957,
Gorilla gorilla	ENSGGOG00000024274	13 retrocopies	retro_ggor_1327, retro_ggor_1611, retro_ggor_1716, retro_ggor_1989, retro_ggor_2029, retro_ggor_2125, retro_ggor_2314, retro_ggor_2473, retro_ggor_39, retro_ggor_524, retro_ggor_552, retro_ggor_654, retro_ggor_771,
Loxodonta africana	ENSLAFG00000004155	1 retrocopy	retro_lafr_677,
Macropus eugenii	ENSMEUG00000014522	3 retrocopies	retro_meug_1678, retro_meug_2006, retro_meug_2112,
Myotis lucifugus	ENSMLUG00000013809	15 retrocopies	retro_mluc_1357, retro_mluc_1709, retro_mluc_1720, retro_mluc_2052, retro_mluc_2142, retro_mluc_2454, retro_mluc_425, retro_mluc_623, retro_mluc_701, retro_mluc_714, retro_mluc_748, retro_mluc_749, retro_mluc_907, retro_mluc_943, retro_mluc_99,
Macaca mulatta	ENSMMUG00000006353	1 retrocopy	retro_mmul_209,
Monodelphis domestica	ENSMODG00000014880	3 retrocopies	retro_mdom_1315, retro_mdom_1803, retro_mdom_918,
Mustela putorius furo	ENSMPUG00000012148	7 retrocopies	retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus	ENSMUSG00000012405	2 retrocopies	retro_mmus_118, retro_mmus_8,
Nomascus leucogenys	ENSNLEG00000003580	1 retrocopy	retro_nleu_80,
Oryctolagus cuniculus	ENSOCUG00000010961	2 retrocopies	retro_ocun_215, retro_ocun_228,
Otolemur garnettii	ENSOGAG00000013056	13 retrocopies	retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Rattus norvegicus	ENSRNOG00000008140	17 retrocopies	retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa	ENSSSCG00000028079	5 retrocopies	retro_sscr_1219 , retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Ictidomys tridecemlineatus	ENSSTOG00000011153	4 retrocopies	retro_itri_1445, retro_itri_1838, retro_itri_479, retro_itri_785,
Tupaia belangeri	ENSTBEG00000009843	34 retrocopies	retro_tbel_1031, retro_tbel_1072, retro_tbel_1322, retro_tbel_1346, retro_tbel_1363, retro_tbel_1524, retro_tbel_1668, retro_tbel_1931, retro_tbel_1980, retro_tbel_2035, retro_tbel_2212, retro_tbel_2270, retro_tbel_2453, retro_tbel_2634, retro_tbel_2818, retro_tbel_3196, retro_tbel_3208, retro_tbel_3387, retro_tbel_3449, retro_tbel_352, retro_tbel_3936, retro_tbel_4079, retro_tbel_4417, retro_tbel_4433, retro_tbel_4477, retro_tbel_4564, retro_tbel_4705, retro_tbel_476, retro_tbel_555, retro_tbel_727, retro_tbel_746, retro_tbel_84, retro_tbel_929, retro_tbel_992,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,