RetrogeneDB ID: retro_sscr_100

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:18889839..18890197(+)
• Located in intron of: ENSSSCG00000004110

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL30
• Ensembl ID: ENSSSCG00000006081
• Aliases: None
• Description: ribosomal protein L30 [Source:HGNC Symbol;Acc:10333]

Sequence

>retro_sscr_100
GTGGTGGTCACAAACAAGACAAAGTTGCCAAAGTCAATCAACTCTAGACTCCAGATCAACTCTAGATTCCAACTCCTTAT
GAAAAACTGGAAAGCACATGCTGAGGCACATGCAGGTTCTAAAAATGATGAGATAAGGCAAAGTGAACTGGTCATCCTCA
CCAACAACTGCTCAGCCTTGAGGAAATCTGTAAGAGAGTATTATGCTATGTTGGCCAAATCCAGTATCTATCCACAGCAG
CAATAATGCTGAATTGGGCATAGCATATAGGAAATACCACAGAATATGCAAACTGGCTATCACTGATCCAGGTGATTCTG
ACATCATTAGATGTATGCTGAAACAGACTGGTGAAAAA

Alignment

ORF - retro_sscr_100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVAAKKTK--KSLES---INSRLQLVM-KSGKYVLGYKQTLKMIRQGK-AKLVILANNCPALRKSEIEYY
          .V...KTK..KS..S...INSR.QL.M.K.GK..L...Q.LKM.R.GK...LVIL.NNC.ALRKS..EYY
Retrocopy VVVTNKTKLPKSINSRLQINSRFQLLM>KTGKHMLRHMQVLKMMR*GK<SELVILTNNCSALRKSVREYY

Parental  AMLAKTGVH-HYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK
          AMLAK.....H.S.NN.ELG.A..KY.R.C.LAI.DPGDSDIIR.M..QTGEK
Retrocopy AMLAKSSIY>H-SSNNAELGIAYRKYHRICKLAITDPGDSDIIRCMLKQTGEK

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	253.65 RPM
SRP014902_testis	0.00 RPM	430.85 RPM
SRP018288_heart	0.03 RPM	290.46 RPM
SRP018288_kidney	0.00 RPM	324.48 RPM
SRP018288_liver	0.00 RPM	330.37 RPM
SRP018288_lung	0.00 RPM	87.98 RPM
SRP018856_adipose	0.00 RPM	1248.10 RPM
SRP035408_brain	0.00 RPM	97.38 RPM
SRP035408_liver	0.00 RPM	85.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_100 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_100 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Gorilla gorilla	ENSGGOG00000005502	9 retrocopies	retro_ggor_1416, retro_ggor_1663, retro_ggor_178, retro_ggor_1925, retro_ggor_2661, retro_ggor_2886, retro_ggor_3073, retro_ggor_46, retro_ggor_866,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Mus musculus	ENSMUSG00000058600	21 retrocopies	retro_mmus_1048, retro_mmus_1102, retro_mmus_1276, retro_mmus_1434, retro_mmus_1439, retro_mmus_1586, retro_mmus_2059, retro_mmus_2273, retro_mmus_2728, retro_mmus_2828, retro_mmus_3179, retro_mmus_3286, retro_mmus_342, retro_mmus_3465, retro_mmus_3573, retro_mmus_3583, retro_mmus_3681, retro_mmus_3691, retro_mmus_569, retro_mmus_789, retro_mmus_892,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Pongo abelii	ENSPPYG00000018774	4 retrocopies	retro_pabe_1605, retro_pabe_178, retro_pabe_2846, retro_pabe_8,
Sus scrofa	ENSSSCG00000006081	6 retrocopies	retro_sscr_100 , retro_sscr_1211, retro_sscr_778, retro_sscr_782, retro_sscr_876, retro_sscr_963,