RetrogeneDB ID: retro_sscr_4

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:21871623..21871935(-)
• Located in intron of: ENSSSCG00000007066

Retrocopy information

• Ensembl ID: ENSSSCG00000007065
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000004970
• Aliases: None
• Description: 60S acidic ribosomal protein P1 [Source:RefSeq peptide;Acc:NP_001123436]

Sequence

>retro_sscr_4
ATGGCCTCCATCTCAGAGCTTTCCTGCATCTATTCTGCCCTCATCCTGCACGATGATGAAGTGATGGTCACAGGGGATAA
GATCAAGTCCCTCATTCATACAGCAAGTGTAAATCATGAGCCTTTCTGGCCAGGCTTGTTTGCAAAGGCTCTGGCCAGTG
TCAACATCAGGAGCCTCATCTGCGATGTGGGGGCTTGGTGGACCTGCCCCAGCAGCAGGTCCTGCCCTATCCAACTGCTG
CCCCAGCTGAGAAGAAAGCTGAAGCAAAGAAAGAAGTCTAATGATGATACGGGCTTTGGTTTTTTTGGCTAA

Alignment

ORF - retro_sscr_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAGGPAP
          MAS.SEL.CIYSALILHDDEV.VT.DKI..LI..A.VN.EPFWPGLFAKALA.VNI.SLIC.VGA....P
Retrocopy MASISELSCIYSALILHDDEVMVTGDKIKSLIHTASVNHEPFWPGLFAKALASVNIRSLICDVGAWWTCP

Parental  AAGAAP
          .....P
Retrocopy SSRSCP

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	0.13 RPM	1617.86 RPM
SRP014902_testis	0.00 RPM	725.90 RPM
SRP018288_heart	0.03 RPM	643.73 RPM
SRP018288_kidney	0.00 RPM	656.64 RPM
SRP018288_liver	0.00 RPM	457.02 RPM
SRP018288_lung	0.10 RPM	934.87 RPM
SRP018856_adipose	0.32 RPM	1028.28 RPM
SRP035408_brain	0.00 RPM	921.91 RPM
SRP035408_liver	0.15 RPM	904.63 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_4 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_4 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014251	20 retrocopies	retro_amel_1030, retro_amel_1076, retro_amel_110, retro_amel_1152, retro_amel_1191, retro_amel_128, retro_amel_1343, retro_amel_1345, retro_amel_1354, retro_amel_1428, retro_amel_161, retro_amel_1694, retro_amel_1696, retro_amel_1705, retro_amel_1852, retro_amel_205, retro_amel_316, retro_amel_395, retro_amel_404, retro_amel_769,
Cavia porcellus	ENSCPOG00000004321	6 retrocopies	retro_cpor_1011, retro_cpor_1058, retro_cpor_260, retro_cpor_305, retro_cpor_667, retro_cpor_75,
Dasypus novemcinctus	ENSDNOG00000014224	26 retrocopies	retro_dnov_1130, retro_dnov_1325, retro_dnov_1410, retro_dnov_1439, retro_dnov_146, retro_dnov_1467, retro_dnov_1580, retro_dnov_1660, retro_dnov_1667, retro_dnov_17, retro_dnov_1748, retro_dnov_179, retro_dnov_1878, retro_dnov_1911, retro_dnov_1967, retro_dnov_20, retro_dnov_2075, retro_dnov_2234, retro_dnov_240, retro_dnov_2421, retro_dnov_2618, retro_dnov_2640, retro_dnov_405, retro_dnov_561, retro_dnov_601, retro_dnov_746,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Macropus eugenii	ENSMEUG00000015282	2 retrocopies	retro_meug_207, retro_meug_45,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Monodelphis domestica	ENSMODG00000009218	4 retrocopies	retro_mdom_1168, retro_mdom_2001, retro_mdom_385, retro_mdom_50,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Sus scrofa	ENSSSCG00000004970	16 retrocopies	retro_sscr_1105, retro_sscr_1165, retro_sscr_1184, retro_sscr_1185, retro_sscr_16, retro_sscr_176, retro_sscr_18, retro_sscr_259, retro_sscr_307, retro_sscr_323, retro_sscr_4 , retro_sscr_47, retro_sscr_583, retro_sscr_776, retro_sscr_904, retro_sscr_923,