RetrogeneDB ID: retro_sscr_1190

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:42045536..42045974(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031057
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSSSCG00000026393
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]

Sequence

>retro_sscr_1190
AGACTCTTATCTTTGGAAATGGCCGACCAGAAGGAGAAACTAAAAATCAAGAAAGCATAGTTGATGAACAAGGTCCTGAA
AAACCCTGAAGATGCCAGCTCTCTGGAGGCTTGAATTGTTGCCCTGACTGTCAAGATACACAATTATGAAGAACATATGC
AAAAACATCAAAAGGACAAAGCCCACATGCACTATCTGCTGATGAGCATTGACCAGAGGAAAAAGATTCTCAAAACTCTC
TGCAAGACAAACTCTGTTGTCTTTAAGAAAATATTCAGGGAGCTGGGTATTGAGTACACCCTTCCCCCATGGTGCTACCA
AAAGCCCACCACCACTGGGTGACCAAGAAGGTTCTGTGCATTCAGGTTTTCCAAGAGGCTCAAAAGCTGAAGAAGCAAAA
ATGGCGCCTTAAAAGCCACAGCTGCCACAGTCCAGAAA

Alignment

ORF - retro_sscr_1190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLLSLEMANQKEKLKIKKMQLMNKVLENPEDTSSLEARIVALTVKIRNYEEHMQKHRKDKAHKRFLLMSI
          RLLSLEMA.QKEKLKIKK..LMNKVL.NPED.SSLEA.IVALTVKI.NYEEHMQKH.KDKAH...LLMSI
Retrocopy RLLSLEMADQKEKLKIKKA*LMNKVLKNPEDASSLEA*IVALTVKIHNYEEHMQKHQKDKAHMHYLLMSI

Parental  DQRKKMLKNLRETNYAVFEKICKELGIEYTFPPPYHR-KAHRRWVTKKALCTQVFREVQKLKKQK-RALR
          DQRKK.LK.L..TN..VF.KI..ELGIEYT.PP.....KAH..WVTKK.LC.QVF.E.QKLKKQK..AL.
Retrocopy DQRKKILKTLCKTNSVVFKKIFRELGIEYTLPPWCYQ<KAHHHWVTKKVLCIQVFQEAQKLKKQK>GALK

Parental  AAAVAAHK
          A.A....K
Retrocopy ATAATVQK

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	6.50 RPM
SRP014902_testis	0.00 RPM	26.45 RPM
SRP018288_heart	0.00 RPM	37.59 RPM
SRP018288_kidney	0.00 RPM	33.69 RPM
SRP018288_liver	0.00 RPM	30.06 RPM
SRP018288_lung	0.00 RPM	23.11 RPM
SRP018856_adipose	0.00 RPM	39.35 RPM
SRP035408_brain	0.00 RPM	53.83 RPM
SRP035408_liver	0.00 RPM	49.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1190 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190 ,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,