RetrogeneDB ID: retro_sscr_1013

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:120158317..120158597(-)
• Located in intron of: ENSSSCG00000025541

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSSSCG00000009146
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_sscr_1013
GCCTCTGGCCAAACTAGGTTGTGTCAAACCCCTGGTAATGAAATTGTTTACTTTTTATACCAGGAAGGTTGGAAAAGCAC
TAAAATCCATATGTAGCATGTGCTCAGGAGTTCGTGTTGTGAGACCTGACATTCTTAGGAGGTCATGTAAAATAGATGTC
AGCAGGGCCTGTGGCAGATGCACCTGTGCTAAGTGAGCCTGTGACAGGATCAAGCTTACTTATTGAGCAGAAACTCTGAT
GAAAATGTTGAAGGCACAAGCACAGAATCAGAACGCTAAA

Alignment

ORF - retro_sscr_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.4 %
• Parental protein coverage: 87.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASNKTRLSRTPGNRIVYL-YTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCA
          AS..TRL..TPGN.IVY..YT.KVGKA.KS.C..C.G....VR.VRP..L.R....K..VSRA.G...CA
Retrocopy ASGQTRLCQTPGNEIVYF>YTRKVGKALKSICSMCSG----VRVVRPDILRR--SCKIDVSRACGRCTCA

Parental  KCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
          K...DRIK.....E......K.LKAQAQ.Q.AK
Retrocopy K*ACDRIKLTY*AE---TLMKMLKAQAQNQNAK

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	100.88 RPM
SRP014902_testis	0.00 RPM	599.73 RPM
SRP018288_heart	0.00 RPM	233.25 RPM
SRP018288_kidney	0.00 RPM	294.53 RPM
SRP018288_liver	0.00 RPM	280.48 RPM
SRP018288_lung	0.00 RPM	321.06 RPM
SRP018856_adipose	0.00 RPM	673.61 RPM
SRP035408_brain	0.73 RPM	263.77 RPM
SRP035408_liver	0.03 RPM	204.49 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1013 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1013 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Equus caballus	ENSECAG00000019719	1 retrocopy	retro_ecab_58,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus	ENSMLUG00000000464	4 retrocopies	retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Sus scrofa	ENSSSCG00000009146	8 retrocopies	retro_sscr_1013 , retro_sscr_1014, retro_sscr_1024, retro_sscr_522, retro_sscr_697, retro_sscr_703, retro_sscr_845, retro_sscr_929,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Tursiops truncatus	ENSTTRG00000003443	6 retrocopies	retro_ttru_1667, retro_ttru_1831, retro_ttru_355, retro_ttru_710, retro_ttru_717, retro_ttru_821,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,