RetrogeneDB ID: retro_sscr_135

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:206384444..206384851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23
• Ensembl ID: ENSSSCG00000021590
• Aliases: None
• Description: Sus scrofa ribosomal protein L23 (RPL23), mRNA. [Source:RefSeq mRNA;Acc:NM_001129955]

Sequence

>retro_sscr_135
AAGCAAAGATGTGGTGGTTCCCTTCATGCAAAATACTGCATTTCCCTGGGTCTTCTAGCAGGAGTCATGATCAACTGTGC
TGTGCCAACACCACCAAAGACAGTTCTGCATATTCTCTGTGAAGTGCAGCAAGGAACGGCTGAACAGACTTCTGCTGGGG
TAGGTGACATGATGGTGGCCACAGTCAGGAAAAGTGGACCAGAACTCAGAGAAGGAAACACATCCAGCAGTGGTAATTCA
ACAACAGAAGGCATCCTGGAGAAAGATGCTGAGTTCCTTTATATTAGCCATCATAGGAAGGTCATAGTGAACAGTAAGTC
AAGATGAAAGATTCTGCCATCATAAGGCCAGCTCCAGAGGTGTGTGCAGACTTGTGGCCCAGGATTTCGTTCAAGGCTGG
CAGCATC

Alignment

ORF - retro_sscr_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.43 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGKPEL
          K...GGS..AK..ISLGL..G..INCA..T..K....I......G.......AGVGDM..ATV.K..PEL
Retrocopy KQRCGGSLHAKYCISLGLLAGVMINCAVPTPPKTVLHILCEVQQGTAEQT-SAGVGDMMVATVRKSGPEL

Parental  R-KKVHPAVVIRQRKSYRR-KDGVFLYFEDNAGVIVNNKG-EMKGSAITGPVAKECADLWPRIASNAGSI
          R.K..HPAVVI.Q.K...R.KD..FLY......VIVN.K...MK.SAI..P....CADLWPRI...AGSI
Retrocopy R>KETHPAVVIQQQKASWR<KDAEFLYISHHRKVIVNSKS<KMKDSAIIRPAPEVCADLWPRISFKAGSI

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	162.46 RPM
SRP014902_testis	0.00 RPM	656.17 RPM
SRP018288_heart	0.00 RPM	596.90 RPM
SRP018288_kidney	0.00 RPM	461.01 RPM
SRP018288_liver	0.00 RPM	455.10 RPM
SRP018288_lung	0.00 RPM	353.13 RPM
SRP018856_adipose	0.00 RPM	896.97 RPM
SRP035408_brain	0.03 RPM	714.29 RPM
SRP035408_liver	0.00 RPM	744.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_135 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_135 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_349

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004268	6 retrocopies	retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Bos taurus	ENSBTAG00000003229	5 retrocopies	retro_btau_1588, retro_btau_349, retro_btau_65, retro_btau_953, retro_btau_974,
Canis familiaris	ENSCAFG00000028955	1 retrocopy	retro_cfam_118,
Choloepus hoffmanni	ENSCHOG00000009153	9 retrocopies	retro_chof_1290, retro_chof_1583, retro_chof_1599, retro_chof_1610, retro_chof_2422, retro_chof_2565, retro_chof_520, retro_chof_872, retro_chof_95,
Callithrix jacchus	ENSCJAG00000008311	9 retrocopies	retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Cavia porcellus	ENSCPOG00000010002	2 retrocopies	retro_cpor_1212, retro_cpor_263,
Latimeria chalumnae	ENSLACG00000004430	1 retrocopy	retro_lcha_16,
Loxodonta africana	ENSLAFG00000028450	4 retrocopies	retro_lafr_274, retro_lafr_305, retro_lafr_375, retro_lafr_440,
Macropus eugenii	ENSMEUG00000001188	2 retrocopies	retro_meug_1717, retro_meug_515,
Macaca mulatta	ENSMMUG00000004502	9 retrocopies	retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Mus musculus	ENSMUSG00000071415	10 retrocopies	retro_mmus_1146, retro_mmus_1430, retro_mmus_2153, retro_mmus_2297, retro_mmus_2319, retro_mmus_2826, retro_mmus_3603, retro_mmus_3704, retro_mmus_583, retro_mmus_657,
Nomascus leucogenys	ENSNLEG00000000642	7 retrocopies	retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Ornithorhynchus anatinus	ENSOANG00000001230	1 retrocopy	retro_oana_76,
Oryctolagus cuniculus	ENSOCUG00000013915	6 retrocopies	retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii	ENSOGAG00000012445	7 retrocopies	retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps	ENSOPRG00000001957	10 retrocopies	retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Pongo abelii	ENSPPYG00000008501	10 retrocopies	retro_pabe_2083, retro_pabe_2085, retro_pabe_2951, retro_pabe_3145, retro_pabe_3147, retro_pabe_3316, retro_pabe_3340, retro_pabe_3362, retro_pabe_455, retro_pabe_512,
Pan troglodytes	ENSPTRG00000009079	9 retrocopies	retro_ptro_1467, retro_ptro_164, retro_ptro_1677, retro_ptro_1679, retro_ptro_2428, retro_ptro_2512, retro_ptro_2513, retro_ptro_2738, retro_ptro_417,
Rattus norvegicus	ENSRNOG00000004107	10 retrocopies	retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Sus scrofa	ENSSSCG00000021590	3 retrocopies	retro_sscr_1115, retro_sscr_135 , retro_sscr_332,
Vicugna pacos	ENSVPAG00000005694	2 retrocopies	retro_vpac_29, retro_vpac_634,