RetrogeneDB ID: retro_sscr_1039

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:121473092..121473457(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000015460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL22L1
• Ensembl ID: ENSSSCG00000027441
• Aliases: None
• Description: ribosomal protein L22-like 1 [Source:HGNC Symbol;Acc:27610]

Sequence

>retro_sscr_1039
ATGGCGCCAAAGAAAGACAAGAAGCCTAAGAAGTCAACCTGGAAGTTTAATTTAGACCTGACTCATCCAGTAGGAGATGG
AATTTTTGATGCTCGAAATTTTGAATAGTTTCTACGGGAAAGGTTAAAGTGAATGGAAAAACTGGAAATCTTGGGAATGT
TGTTCACATTGAACACTTCAAGAATAAAATCATGGTTGTTTCTGAGAAACAGTTCTCTAAAAGATATTTGAAATATCTTA
CCAAGAAATACCTTAAGAAGAACAATCTTCATGATTGGCATCGTGTGGTTGCATCTGACAAGGAGACCTATGAATTTCGT
TACTTCCAGATTAGTCAAGATGAAGATGGATCAGAGTCTGAGGAC

Alignment

ORF - retro_sscr_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPKKDKKPKKSTWKFNLDLTHPVEDGIFDARNFEQFLRE-KVKVNGKTGNLGNVVHIEHFKNKIMVVSE
          MAPKKDKKPKKSTWKFNLDLTHPV.DGIFDARNFE.FLRE.KVKVNGKTGNLGNVVHIEHFKNKIMVVSE
Retrocopy MAPKKDKKPKKSTWKFNLDLTHPVGDGIFDARNFE*FLRE<KVKVNGKTGNLGNVVHIEHFKNKIMVVSE

Parental  KQFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSESED
          KQFSKRYLKYLTKKYLKKNNL.DW.RVVASDKETYE.RYFQISQDEDGSESED
Retrocopy KQFSKRYLKYLTKKYLKKNNLHDWHRVVASDKETYEFRYFQISQDEDGSESED

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	3.45 RPM
SRP014902_testis	0.14 RPM	41.73 RPM
SRP018288_heart	0.00 RPM	12.65 RPM
SRP018288_kidney	0.00 RPM	16.25 RPM
SRP018288_liver	0.00 RPM	17.91 RPM
SRP018288_lung	0.00 RPM	5.70 RPM
SRP018856_adipose	0.00 RPM	12.94 RPM
SRP035408_brain	0.03 RPM	17.09 RPM
SRP035408_liver	0.00 RPM	34.29 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1039 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1039 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004730	1 retrocopy	retro_amel_7,
Canis familiaris	ENSCAFG00000014955	2 retrocopies	retro_cfam_1410, retro_cfam_773,
Callithrix jacchus	ENSCJAG00000002427	1 retrocopy	retro_cjac_3983,
Cavia porcellus	ENSCPOG00000009215	1 retrocopy	retro_cpor_1544,
Equus caballus	ENSECAG00000018894	1 retrocopy	retro_ecab_728,
Erinaceus europaeus	ENSEEUG00000011941	5 retrocopies	retro_eeur_436, retro_eeur_60, retro_eeur_602, retro_eeur_676, retro_eeur_691,
Echinops telfairi	ENSETEG00000010658	9 retrocopies	retro_etel_1289, retro_etel_1433, retro_etel_1459, retro_etel_151, retro_etel_1680, retro_etel_335, retro_etel_513, retro_etel_800, retro_etel_936,
Homo sapiens	ENSG00000163584	1 retrocopy	retro_hsap_2929,
Gorilla gorilla	ENSGGOG00000001734	1 retrocopy	retro_ggor_2031,
Gadus morhua	ENSGMOG00000004077	1 retrocopy	retro_gmor_10,
Loxodonta africana	ENSLAFG00000013220	2 retrocopies	retro_lafr_1121, retro_lafr_682,
Macropus eugenii	ENSMEUG00000009484	1 retrocopy	retro_meug_390,
Myotis lucifugus	ENSMLUG00000023052	2 retrocopies	retro_mluc_1183, retro_mluc_1588,
Myotis lucifugus	ENSMLUG00000027683	8 retrocopies	retro_mluc_1225, retro_mluc_1403, retro_mluc_1690, retro_mluc_1804, retro_mluc_1967, retro_mluc_2383, retro_mluc_2401, retro_mluc_668,
Macaca mulatta	ENSMMUG00000022881	2 retrocopies	retro_mmul_1927, retro_mmul_1954,
Mus musculus	ENSMUSG00000039221	4 retrocopies	retro_mmus_1380, retro_mmus_2633, retro_mmus_2674, retro_mmus_3631,
Nomascus leucogenys	ENSNLEG00000005287	2 retrocopies	retro_nleu_1918, retro_nleu_2266,
Oryctolagus cuniculus	ENSOCUG00000014962	2 retrocopies	retro_ocun_1, retro_ocun_256,
Otolemur garnettii	ENSOGAG00000012642	2 retrocopies	retro_ogar_1434, retro_ogar_780,
Procavia capensis	ENSPCAG00000008704	1 retrocopy	retro_pcap_105,
Pongo abelii	ENSPPYG00000025900	1 retrocopy	retro_pabe_2524,
Pteropus vampyrus	ENSPVAG00000011524	1 retrocopy	retro_pvam_328,
Rattus norvegicus	ENSRNOG00000011817	2 retrocopies	retro_rnor_111, retro_rnor_2152,
Sus scrofa	ENSSSCG00000003367	4 retrocopies	retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,
Sus scrofa	ENSSSCG00000027441	5 retrocopies	retro_sscr_1039 , retro_sscr_129, retro_sscr_141, retro_sscr_85, retro_sscr_860,
Ictidomys tridecemlineatus	ENSSTOG00000022972	3 retrocopies	retro_itri_1511, retro_itri_1533, retro_itri_492,
Tupaia belangeri	ENSTBEG00000000357	17 retrocopies	retro_tbel_1135, retro_tbel_1188, retro_tbel_2011, retro_tbel_2073, retro_tbel_2081, retro_tbel_226, retro_tbel_2325, retro_tbel_2333, retro_tbel_2434, retro_tbel_2936, retro_tbel_3526, retro_tbel_3796, retro_tbel_4070, retro_tbel_4372, retro_tbel_4573, retro_tbel_4681, retro_tbel_575,
Tursiops truncatus	ENSTTRG00000007035	3 retrocopies	retro_ttru_1180, retro_ttru_168, retro_ttru_968,