RetrogeneDB ID: retro_sscr_856

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:16631531..16632206(-)
• Located in intron of: ENSSSCG00000028109

Retrocopy information

• Ensembl ID: ENSSSCG00000022800
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000005169
• Aliases: None
• Description: 40S ribosomal protein S6 [Source:UniProtKB/TrEMBL;Acc:F2Z5Q6]

Sequence

>retro_sscr_856
AAGAACAAAACCTTTGTAGATGAAGGTGCAACAGAAGTTGCTGCTGATGCTCTGGGTGAAGAATGGAAGGGTGATGTGGT
CCGGATCAGTGGTGGGAAGGACAAACAGGGTTTCCCCATGAAGCAGGGTGTCTTGACCCAGGCTGAGTCCACCTGCTACT
GAGGAAGGGGCGTTCCTGTTACAGACCAAGGAGGACTGGAGAAACAAAGTGCACATCGGTTCGGGGTTGCATTGTGGATG
CCAATCTCAGTGTTCTCAATTTGGTCATCATAAAAAAAGGGGAGAAGGGTATTCCTGGACTCACCGATACTACTGTGCCT
CACTGCCTGGGGCCTAAAAGAGCTAGCAGAATCCACAACTTCTCAGTCTCTCTGAAGAAGAGGATGTCCATCAGTATGCA
GTGAAAAAGCCCCTAAACAAAGAAGGTAAGACGCCTAGGACCAAAGCACCCGAGATGCAGCGTCTTGTTACTCCACGTGC
TTGGCAACACAAATGTCAGCGTATTGCTCTGAAGAAACAACGTACTAAGAAAAATAAGGAAGACGCTGCAGAATATGCTA
AACTTTTGGCCAAGAGAATGAAGGATGCCAAAGGAAAACATCAGGAACAGATTGCCAAGAGACAGAGGCTATCTCCTCTG
AAGCTTCTACCTACAAGTCTGAGTCCAGTCAAAAG

Alignment

ORF - retro_sscr_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH-GRVRLLLSKGHSCYRPRRTGE
          K..TF.....ATEVAADALGEEWKG.VVRISGG.DKQGFPMKQGVLT..G.V.LLL.KG.SCYRPRRTGE
Retrocopy KNKTFVDEG-ATEVAADALGEEWKGDVVRISGGKDKQGFPMKQGVLTQ<G*VHLLLRKGRSCYRPRRTGE

Parental  RKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIR-KLFNLSKEDDVRQYVVRK
          .K..SVRGCIVDANLSVLNLVI.KKGEK.IPGLTDTTVP..LGPKRASRI...L..LS.E.DV.QY.V.K
Retrocopy TKCTSVRGCIVDANLSVLNLVIIKKGEKGIPGLTDTTVPHCLGPKRASRIH<QLLSLSEEEDVHQYAVKK

Parental  PLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAK
          PLNKEGK.PRTKAP..QRLVTPR..QHK..RIALKKQRTKKNKE.AAEYAKLLAKRMK.AK.K.QEQIAK
Retrocopy PLNKEGKTPRTKAPEMQRLVTPRAWQHKCQRIALKKQRTKKNKEDAAEYAKLLAKRMKDAKGKHQEQIAK

Parental  RRRLSSLR-ASTSKSESSQK
          R.RLS.L..AST.KSESSQK
Retrocopy RQRLSPLK<ASTYKSESSQK

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	588.80 RPM
SRP014902_testis	0.57 RPM	637.50 RPM
SRP018288_heart	0.03 RPM	741.67 RPM
SRP018288_kidney	0.30 RPM	539.22 RPM
SRP018288_liver	0.32 RPM	510.91 RPM
SRP018288_lung	0.31 RPM	379.81 RPM
SRP018856_adipose	0.20 RPM	2012.73 RPM
SRP035408_brain	0.64 RPM	937.54 RPM
SRP035408_liver	0.06 RPM	1350.54 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_856 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Ailuropoda melanoleuca	ENSAMEG00000002925	14 retrocopies	retro_amel_1040, retro_amel_1250, retro_amel_1384, retro_amel_1526, retro_amel_1646, retro_amel_1676, retro_amel_189, retro_amel_312, retro_amel_334, retro_amel_382, retro_amel_510, retro_amel_568, retro_amel_657, retro_amel_841,
Canis familiaris	ENSCAFG00000001615	4 retrocopies	retro_cfam_184, retro_cfam_1936, retro_cfam_48, retro_cfam_87,
Callithrix jacchus	ENSCJAG00000020612	6 retrocopies	retro_cjac_1246, retro_cjac_18, retro_cjac_180, retro_cjac_190, retro_cjac_2982, retro_cjac_59,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Equus caballus	ENSECAG00000016190	5 retrocopies	retro_ecab_175, retro_ecab_312, retro_ecab_603, retro_ecab_771, retro_ecab_861,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Felis catus	ENSFCAG00000002541	26 retrocopies	retro_fcat_1082, retro_fcat_1108, retro_fcat_1154, retro_fcat_1262, retro_fcat_1373, retro_fcat_1642, retro_fcat_1679, retro_fcat_1760, retro_fcat_1791, retro_fcat_1934, retro_fcat_1937, retro_fcat_1963, retro_fcat_198, retro_fcat_238, retro_fcat_328, retro_fcat_358, retro_fcat_380, retro_fcat_392, retro_fcat_493, retro_fcat_659, retro_fcat_738, retro_fcat_750, retro_fcat_850, retro_fcat_894, retro_fcat_912, retro_fcat_968,
Gorilla gorilla	ENSGGOG00000002652	13 retrocopies	retro_ggor_1430, retro_ggor_1703, retro_ggor_2097, retro_ggor_2358, retro_ggor_2439, retro_ggor_2769, retro_ggor_2863, retro_ggor_2864, retro_ggor_616, retro_ggor_670, retro_ggor_777, retro_ggor_896, retro_ggor_965,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Macaca mulatta	ENSMMUG00000003412	1 retrocopy	retro_mmul_263,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Sus scrofa	ENSSSCG00000005169	6 retrocopies	retro_sscr_187, retro_sscr_425, retro_sscr_645, retro_sscr_856 , retro_sscr_940, retro_sscr_983,