RetrogeneDB ID: retro_sscr_209

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:297341363..297341775(-)
• Located in intron of: ENSSSCG00000020743

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006182
• Aliases: None
• Description: Ribosomal protein L7 [Source:UniProtKB/TrEMBL;Acc:A8YQT8]

Sequence

>retro_sscr_209
ATGGCTAGGATAGCAAGAAAAGCTGGCAACTTCTAAGTACTTGCAGAACCCCAACTGGCATTTGTCATCAGGAACCCTGG
TACCAATGTTGTGAGCCCAAAGGTCCAAAAGGTGTCGCAGCTTCTCTGCCTCCATCAGATCTTCAGTGGCAACTGTGTGA
AGCTCAACAAGGCTTAAATTAACATGCTGAGAATTGTGGAACCATATATTGTATGGGGGTACCCAAATCTGAGGTCAGTA
AATGAAGTGATCTACAAGTGTGGTTATGGCAAAATCAACAAGAAGTCAACTGCCCTGACAGATAACACATTGATTGTTTG
ATCTCTTGGTAAATACAGCATCATCTACATGGAGGATCTGATTCATGAGATCTACTGTTGGAAAATGTTTCAAAGAAGCA
AACAACTTCCTG

Alignment

ORF - retro_sscr_209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.26 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYI
          MAR.ARKAGNF.V.AEP.LAFVIR..G.N.VSPKV.KV.QLL.L.QIF.G..VKLNKA.INMLRIVEPYI
Retrocopy MARIARKAGNF*VLAEPQLAFVIRNPGTNVVSPKVQKVSQLLCLHQIFSGNCVKLNKA*INMLRIVEPYI

Parental  AWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFK-EANNFL
          .WGYPNL.SVNE.IYK.GYGKINKK..ALTDN.LI..SLGKY.II.MEDLIHEIY...K.F..EANNFL
Retrocopy VWGYPNLRSVNEVIYKCGYGKINKKSTALTDNTLIV*SLGKYSIIYMEDLIHEIY-CWKMFQ>EANNFL

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	366.21 RPM
SRP014902_testis	0.99 RPM	1177.26 RPM
SRP018288_heart	0.10 RPM	779.39 RPM
SRP018288_kidney	0.10 RPM	476.18 RPM
SRP018288_liver	0.00 RPM	369.23 RPM
SRP018288_lung	0.20 RPM	408.93 RPM
SRP018856_adipose	0.02 RPM	1726.31 RPM
SRP035408_brain	0.16 RPM	332.56 RPM
SRP035408_liver	0.09 RPM	242.63 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_209 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_209 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001821	5 retrocopies	retro_amel_1230, retro_amel_1632, retro_amel_760, retro_amel_933, retro_amel_937,
Canis familiaris	ENSCAFG00000008021	28 retrocopies	retro_cfam_1039, retro_cfam_1075, retro_cfam_1079, retro_cfam_1167, retro_cfam_1209, retro_cfam_1236, retro_cfam_1270, retro_cfam_1308, retro_cfam_1390, retro_cfam_1436, retro_cfam_1445, retro_cfam_1453, retro_cfam_1524, retro_cfam_1541, retro_cfam_1699, retro_cfam_1755, retro_cfam_1855, retro_cfam_1856, retro_cfam_2051, retro_cfam_2192, retro_cfam_338, retro_cfam_403, retro_cfam_563, retro_cfam_609, retro_cfam_737, retro_cfam_74, retro_cfam_922, retro_cfam_998,
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Felis catus	ENSFCAG00000028446	6 retrocopies	retro_fcat_1643, retro_fcat_230, retro_fcat_255, retro_fcat_338, retro_fcat_342, retro_fcat_945,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287, retro_pvam_308, retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209 , retro_sscr_796,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,