RetrogeneDB ID: retro_sscr_578

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:5152463..5152958(-)
• Located in intron of: ENSSSCG00000006981

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL6
• Ensembl ID: ENSSSCG00000024825
• Aliases: None
• Description: Sus scrofa ribosomal protein L6 (RPL6), mRNA. [Source:RefSeq mRNA;Acc:NM_001044542]

Sequence

>retro_sscr_578
CAGCTGCTGAGTCAAGCCAAAAACCCTTCAGTAAGCATGTGAGAAAAACTGCAGGTGAGCATCACTCCTGGGACCATTCT
GATCATCCTCGCTGGGCGCCACGGAGGCAAGAGGGCCATTTTCCTGAAGCGGCTGAGCAGCGGCTCGCTACTTGAGACTG
GTGCCCTACCTTTCAATTGAGTTCCTCTGCAGAGAACACACCAGAAATTTGTCATTGTCACCGCCACCAAAATTGATACC
AGTGATGCGAAAATCCCAGGACATCTCACTGACACTTACTTTAAGCAGAAGAAGCTACATAAGCCCAGGCACCAGGAAGG
TGAGAGCTTGGATGTGGAGAAAGAGAAATACAAGACTACAGAACAGCACAAGGTTGATCAGAAATCTGTGAACTCACAAA
TTCTGTGATGAATCAAAGCTGTTCCTCAGCTCCAAGGCTACCTCTCCTCTGCGTCTGCTCTCACAAAATGGAATTATCCT
CACAAATTGGTATTC

Alignment

ORF - retro_sscr_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 58.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLLSHGK-KPFSKHVRK-LRASITPGTILIILTGRHRGKRVIFLKQLSSGLLLVTGPLSLNRVPLRRTHQ
          .LLS..K.KPFSKHVRK.L..SITPGTILIIL.GRH.GKR.IFLK.LSSG.LL.TG.L..N.VPL.RTHQ
Retrocopy QLLSQAK<KPFSKHVRK>LQVSITPGTILIILAGRHGGKRAIFLKRLSSGSLLETGALPFN*VPLQRTHQ

Parental  KFVIATSTKIDISGVKIPEHLTDAYFKKKKLRKPRHQEGEIFDTEKEKYEISEQRKVDQKAVDSQILRRI
          KFVI.T.TKID.S..KIP.HLTD.YFK.KKL.KPRHQEGE..D.EKEKY...EQ.KVDQK.V.SQIL..I
Retrocopy KFVIVTATKIDTSDAKIPGHLTDTYFKQKKLHKPRHQEGESLDVEKEKYKTTEQHKVDQKSVNSQIL**I

Parental  KAVPQLQGYLRSVFALTNGIYPHKLVF
          KAVPQLQGYL.S..ALT...YPHKLVF
Retrocopy KAVPQLQGYLSSASALTKWNYPHKLVF

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	482.61 RPM
SRP014902_testis	0.28 RPM	1227.90 RPM
SRP018288_heart	0.05 RPM	833.48 RPM
SRP018288_kidney	0.00 RPM	612.90 RPM
SRP018288_liver	0.00 RPM	486.29 RPM
SRP018288_lung	0.00 RPM	983.64 RPM
SRP018856_adipose	0.18 RPM	2000.01 RPM
SRP035408_brain	0.00 RPM	913.88 RPM
SRP035408_liver	0.00 RPM	532.04 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_578 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003060	1 retrocopy	retro_acar_171,
Bos taurus	ENSBTAG00000031723	6 retrocopies	retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris	ENSCAFG00000008873	1 retrocopy	retro_cfam_36,
Callithrix jacchus	ENSCJAG00000012450	7 retrocopies	retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus	ENSCPOG00000013526	8 retrocopies	retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Equus caballus	ENSECAG00000017514	1 retrocopy	retro_ecab_811,
Felis catus	ENSFCAG00000006858	12 retrocopies	retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Gorilla gorilla	ENSGGOG00000003372	16 retrocopies	retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta	ENSMMUG00000007433	1 retrocopy	retro_mmul_171,
Monodelphis domestica	ENSMODG00000003096	4 retrocopies	retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furo	ENSMPUG00000002526	9 retrocopies	retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus	ENSMUSG00000029614	13 retrocopies	retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys	ENSNLEG00000027093	2 retrocopies	retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus	ENSOCUG00000003802	5 retrocopies	retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii	ENSPPYG00000025855	13 retrocopies	retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus	ENSRNOG00000025936	1 retrocopy	retro_rnor_129,
Sarcophilus harrisii	ENSSHAG00000007096	2 retrocopies	retro_shar_506, retro_shar_536,
Sus scrofa	ENSSSCG00000024825	4 retrocopies	retro_sscr_1086, retro_sscr_1137, retro_sscr_397, retro_sscr_578 ,
Ictidomys tridecemlineatus	ENSSTOG00000009409	3 retrocopies	retro_itri_1024, retro_itri_1125, retro_itri_684,
Tursiops truncatus	ENSTTRG00000009268	7 retrocopies	retro_ttru_1053, retro_ttru_1428, retro_ttru_1827, retro_ttru_424, retro_ttru_608, retro_ttru_652, retro_ttru_954,
Vicugna pacos	ENSVPAG00000007000	5 retrocopies	retro_vpac_100, retro_vpac_184, retro_vpac_374, retro_vpac_623, retro_vpac_75,