RetrogeneDB ID: retro_sscr_1154

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:43972664..43973056(+)
• Located in intron of: ENSSSCG00000021846

Retrocopy information

• Ensembl ID: ENSSSCG00000030862
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSSSCG00000025507
• Aliases: None
• Description: Sus scrofa ribosomal protein L27 (RPL27), mRNA. [Source:RefSeq mRNA;Acc:NM_001097479]

Sequence

>retro_sscr_1154
ATGGGCAAGTTCATGAAACCAGGGAAGGTGGTGCTGGTCCTGGCTGGTTGCTACTCCAGATGCAAAGCGGTCATTGTAAA
AAACATTGATGATGGCACCTCAGACCAACCCTATAGCCACGCTCTGGTGACTGGAATTGATTGCTGTCCCACACAGTGAC
AGCTGCCATGGGCAAGAAGAAAACTGCCAAGAGGTCAAAGATGAAGTCTTTTGTGAAAGTTTATAATCACATCATGCCCA
CAAGGTACATCCCCTTAGACAAAACTGTTGTCCATAAGGAGGTGTTCGGAGACCATGCTCTCAAACTCAAGGCTCGGCAA
GAGGCCAAGATCAAGTTCTAGGAAAGATTCAAAACCAGCAAAAACAAATGGTTCTTCCAGAAGCTGCAGTTT

Alignment

ORF - retro_sscr_1154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDG-SDRPYSHALVAGIDRYPRK-VTAAMGKKKIAKRSKIK
          MGKFMKPGKVVLVLAG.YS..KAVIVKNIDDG.SD.PYSHALV.GID..P...VTAAMGKKK.AKRSK.K
Retrocopy MGKFMKPGKVVLVLAGCYSRCKAVIVKNIDDGTSDQPYSHALVTGIDCCPTQ<VTAAMGKKKTAKRSKMK

Parental  SFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
          SFVKVYN..H.MPTRY...IPLDKTVV.K.VF.D.ALK.KAR.EAK.KF.ER.KT.KNKWFFQKL.F
Retrocopy SFVKVYN--HIMPTRY---IPLDKTVVHKEVFGDHALKLKARQEAKIKF*ERFKTSKNKWFFQKLQF

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	217.41 RPM
SRP014902_testis	0.14 RPM	272.57 RPM
SRP018288_heart	0.00 RPM	174.45 RPM
SRP018288_kidney	0.00 RPM	187.26 RPM
SRP018288_liver	0.00 RPM	163.43 RPM
SRP018288_lung	0.00 RPM	86.45 RPM
SRP018856_adipose	0.00 RPM	318.32 RPM
SRP035408_brain	0.00 RPM	226.17 RPM
SRP035408_liver	0.00 RPM	191.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1154 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1154 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Equus caballus	ENSECAG00000007500	1 retrocopy	retro_ecab_132,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mustela putorius furo	ENSMPUG00000009913	11 retrocopies	retro_mputfur_1041, retro_mputfur_1108, retro_mputfur_1182, retro_mputfur_1307, retro_mputfur_1530, retro_mputfur_303, retro_mputfur_413, retro_mputfur_595, retro_mputfur_675, retro_mputfur_735, retro_mputfur_980,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Otolemur garnettii	ENSOGAG00000003940	14 retrocopies	retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sorex araneus	ENSSARG00000011131	10 retrocopies	retro_sara_254, retro_sara_292, retro_sara_493, retro_sara_498, retro_sara_547, retro_sara_611, retro_sara_62, retro_sara_672, retro_sara_685, retro_sara_696,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Sus scrofa	ENSSSCG00000025507	5 retrocopies	retro_sscr_109, retro_sscr_1154 , retro_sscr_576, retro_sscr_683, retro_sscr_943,
Tursiops truncatus	ENSTTRG00000011739	2 retrocopies	retro_ttru_1049, retro_ttru_1535,
Vicugna pacos	ENSVPAG00000002574	1 retrocopy	retro_vpac_324,