RetrogeneDB ID: retro_sscr_145

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:286957899..286958310(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSSSCG00000022357
• Aliases: None
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_sscr_145
AGTGATACAATAGAAAATATAAATGCTAAGATCCAGGATAAGGAAGGAATTCCTCCTGACCAGCAAAGACTGATCTCTGC
TGGCAAGCAACTGGAAGATGGACGTACTTTGTCTGACTACAACATTCAAAAGGAGTCCACTCTTCATCTTGCACTGGAGA
CTTGGTGGTGGTGCTAAGAAAAGGAAGAAGAAGTCTTACACACTCCCAAGAAGAACAAGCATAAGAGAAAGAAGGTTAAG
CTGGCTGTCCTGAAACACTATAAGGTGGACGAGGACGGCAAAATCAGTCGTCTTCGTCGGGAGTGCCCTTCAGCTGAATG
CAGTGCTGGAGTCTTTATGGCCAGCCACTTTGACAGACGTTATTGTGGCAAATGTTGCCTGACCTATTGTTTCAACAAAC
CAGAAGACAAG

Alignment

ORF - retro_sscr_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 87.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL-RLRGGAKKRKKKSYT-T
          SDTIEN..AKIQDKEGIPPDQQRLI.AGKQLEDGRTLSDYNIQKESTLHL.L.RL.GGAKKRKKKSYT.T
Retrocopy SDTIENINAKIQDKEGIPPDQQRLISAGKQLEDGRTLSDYNIQKESTLHLAL>RLGGGAKKRKKKSYT<T

Parental  PKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK
          PKKNKHKRKKVKLAVLK.YKVDE.GKISRLRRECPS.EC.AGVFMASHFDR.YCGKCCLTYCFNKPEDK
Retrocopy PKKNKHKRKKVKLAVLKHYKVDEDGKISRLRRECPSAECSAGVFMASHFDRRYCGKCCLTYCFNKPEDK

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	284.58 RPM
SRP014902_testis	0.42 RPM	884.89 RPM
SRP018288_heart	0.00 RPM	447.20 RPM
SRP018288_kidney	0.20 RPM	497.06 RPM
SRP018288_liver	0.48 RPM	388.10 RPM
SRP018288_lung	0.10 RPM	103.35 RPM
SRP018856_adipose	0.09 RPM	506.66 RPM
SRP035408_brain	0.22 RPM	503.50 RPM
SRP035408_liver	0.23 RPM	403.11 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_145 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_145 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Felis catus	ENSFCAG00000023939	1 retrocopy	retro_fcat_1542,
Homo sapiens	ENSG00000143947	10 retrocopies	retro_hsap_1694, retro_hsap_1715, retro_hsap_2217, retro_hsap_2416, retro_hsap_276, retro_hsap_3344, retro_hsap_3508, retro_hsap_4272, retro_hsap_4649, retro_hsap_4650,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Macropus eugenii	ENSMEUG00000008917	13 retrocopies	retro_meug_107, retro_meug_1184, retro_meug_1460, retro_meug_1514, retro_meug_1544, retro_meug_1657, retro_meug_183, retro_meug_1866, retro_meug_209, retro_meug_521, retro_meug_594, retro_meug_937, retro_meug_94,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Mustela putorius furo	ENSMPUG00000010468	6 retrocopies	retro_mputfur_1512, retro_mputfur_242, retro_mputfur_319, retro_mputfur_332, retro_mputfur_499, retro_mputfur_777,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Sus scrofa	ENSSSCG00000022357	1 retrocopy	retro_sscr_145 ,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,
Tursiops truncatus	ENSTTRG00000013947	5 retrocopies	retro_ttru_1199, retro_ttru_1279, retro_ttru_533, retro_ttru_705, retro_ttru_838,