RetrogeneDB ID: retro_sscr_1172

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:108384248..108384615(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030951
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSSSCG00000015103
• Aliases: None
• Description: ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]

Sequence

>retro_sscr_1172
CCGCCCAAGGACGACAAGAAGAAGAAAGATGCCGGAAAGTTGGCCAAGAAAGACAAAGACCCAGTGAACAAATCTGGGGG
CAAGGCCAAAAAGAAGTGGTCCAAAGGCAAAATTCGGGACAAGCTCAATAATTTAGTCTTGTTTGACAAAGCGACATATG
ACAAACTCTGTAAAGAAGTTCCCAACTATAAGCTTATTACTCCAGCTGTTGTCTCTGAGACTGAAGATTCGTGGTTCTCT
GGCCAGGGCAGCCCTTCAGGAGCTCTTGAGCAAAGGACTTATTAAACTGGTTTCAAAGCACAGAGCTCAAGTAGTTTACA
CCTGAAATACCAAGGGTGGAGATGCCCCAGCTGCTGGAGAAGATGCA

Alignment

ORF - retro_sscr_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEV-PNYKLITP
          PPKDDKKKKDAGK.AKKDKDPVNKSGGKAKKK.WSKGK.RDKLNNLVLFDKATYDKLCKEV.P...L...
Retrocopy PPKDDKKKKDAGKLAKKDKDPVNKSGGKAKKK-WSKGKIRDKLNNLVLFDKATYDKLCKEV>PTISLLLQ

Parental  AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          ...S.RLKIRGSLARAALQELLSKGLIKLVSKHRAQV.YT.NTKGGDAPAAGEDA
Retrocopy -LLSLRLKIRGSLARAALQELLSKGLIKLVSKHRAQVVYT*NTKGGDAPAAGEDA

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	0.66 RPM	132.07 RPM
SRP014902_testis	4.10 RPM	197.60 RPM
SRP018288_heart	0.60 RPM	362.18 RPM
SRP018288_kidney	3.84 RPM	263.80 RPM
SRP018288_liver	4.64 RPM	277.28 RPM
SRP018288_lung	0.20 RPM	251.21 RPM
SRP018856_adipose	1.21 RPM	387.94 RPM
SRP035408_brain	2.35 RPM	195.36 RPM
SRP035408_liver	2.14 RPM	201.79 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1172 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000051	5 retrocopies	retro_amel_1654, retro_amel_1765, retro_amel_574, retro_amel_60, retro_amel_684,
Canis familiaris	ENSCAFG00000012395	3 retrocopies	retro_cfam_500, retro_cfam_680, retro_cfam_984,
Cavia porcellus	ENSCPOG00000013298	2 retrocopies	retro_cpor_705, retro_cpor_9,
Felis catus	ENSFCAG00000001151	3 retrocopies	retro_fcat_1792, retro_fcat_601, retro_fcat_903,
Loxodonta africana	ENSLAFG00000017117	6 retrocopies	retro_lafr_1074, retro_lafr_270, retro_lafr_387, retro_lafr_431, retro_lafr_478, retro_lafr_90,
Microcebus murinus	ENSMICG00000002687	8 retrocopies	retro_mmur_1023, retro_mmur_1514, retro_mmur_229, retro_mmur_308, retro_mmur_387, retro_mmur_425, retro_mmur_485, retro_mmur_688,
Myotis lucifugus	ENSMLUG00000004752	15 retrocopies	retro_mluc_1166, retro_mluc_1482, retro_mluc_1514, retro_mluc_1541, retro_mluc_1665, retro_mluc_1762, retro_mluc_1794, retro_mluc_1947, retro_mluc_2030, retro_mluc_2394, retro_mluc_467, retro_mluc_523, retro_mluc_649, retro_mluc_669, retro_mluc_903,
Monodelphis domestica	ENSMODG00000013334	2 retrocopies	retro_mdom_1267, retro_mdom_1615,
Mustela putorius furo	ENSMPUG00000004960	4 retrocopies	retro_mputfur_1288, retro_mputfur_372, retro_mputfur_525, retro_mputfur_671,
Sus scrofa	ENSSSCG00000015103	12 retrocopies	retro_sscr_1020, retro_sscr_1034, retro_sscr_1035, retro_sscr_1055, retro_sscr_1079, retro_sscr_1107, retro_sscr_1172 , retro_sscr_223, retro_sscr_368, retro_sscr_594, retro_sscr_717, retro_sscr_930,