RetrogeneDB ID: retro_sscr_92

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:125424061..125424493(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000024660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSSSCG00000014133
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_sscr_92
ATGGGCAAGTGTCACGGTCTTCGTACTTCCAGGAAGCTCCGTAGCCACCAACGGGACCAGAAGTGGCACGATAAACAGTA
CAAGAAAGCCCATTTGGGCACAGCCCTGAAGGCCAACCCTTTCGGAGGCGCTTCTCATGCCAAGGGAATTGTGCTTAAAA
AAGTAGGGGTTGAAGCCAAACAGCCAAATTCTGCCATCAGGAAGTGTGTCAGGGTTCAGCTAATCAAGAATGGGAAAAAA
ATTACAGCCTTTGTACCCAATGATGGTTGTTTGAACTTCATTGAGGAAAATGATGAAGTTCTGGTTGCTGGATTTGGTCG
CAAAGGTCATGCTGTTGGTGACATTCCTGGAGTCCACTTTAAGGTTGTCAAAGTAGCCAATGTCTCTCTTTTGGCCTTAT
ACAAAGGCAAGAAGGAGAGACCAAGATCATAA

Alignment

ORF - retro_sscr_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCV
          MGKC.GLRT.RKLRSH.RDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVL.KVGVEAKQPNSAIRKCV
Retrocopy MGKCHGLRTSRKLRSHQRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLKKVGVEAKQPNSAIRKCV

Parental  RVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKER
          RVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGV.FKVVKVANVSLLALYKGKKER
Retrocopy RVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVHFKVVKVANVSLLALYKGKKER

Parental  PRS
          PRS
Retrocopy PRS

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	0.93 RPM	98.75 RPM
SRP014902_testis	6.93 RPM	278.37 RPM
SRP018288_heart	0.81 RPM	210.75 RPM
SRP018288_kidney	1.38 RPM	278.18 RPM
SRP018288_liver	1.44 RPM	284.48 RPM
SRP018288_lung	0.20 RPM	39.92 RPM
SRP018856_adipose	1.57 RPM	615.95 RPM
SRP035408_brain	1.43 RPM	127.74 RPM
SRP035408_liver	2.08 RPM	131.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_92 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_92 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_92 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Dipodomys ordii	ENSDORG00000001813	2 retrocopies	retro_dord_187, retro_dord_93,
Homo sapiens	ENSG00000186468	6 retrocopies	retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287, retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla	ENSGGOG00000025014	6 retrocopies	retro_ggor_1316, retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Macropus eugenii	ENSMEUG00000012931	1 retrocopy	retro_meug_811,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Monodelphis domestica	ENSMODG00000020255	3 retrocopies	retro_mdom_1518, retro_mdom_1612, retro_mdom_395,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Nomascus leucogenys	ENSNLEG00000013203	3 retrocopies	retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Pteropus vampyrus	ENSPVAG00000002083	4 retrocopies	retro_pvam_1483, retro_pvam_782, retro_pvam_80, retro_pvam_922,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92 ,
Vicugna pacos	ENSVPAG00000009427	7 retrocopies	retro_vpac_195, retro_vpac_239, retro_vpac_393, retro_vpac_543, retro_vpac_56, retro_vpac_598, retro_vpac_81,