RetrogeneDB ID: retro_sscr_907

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:73344557..73344776(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPG
• Ensembl ID: ENSSSCG00000024776
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide G [Source:HGNC Symbol;Acc:11163]

Sequence

>retro_sscr_907
GTGAACAGGGCTCACCCTGCTGAAGTGAAAAAAATGTGTGGACAAGAAATTATCACTGAAATCAAGTAGTGGACATGTCC
AAGGAATCTTGGGGGATTTGATCCTTTTATGAACCTTGCAATAGATGACTGTGCAGAGATGGCAACTACTGGGTGAGAGA
ACAATACTAAAATGGCAATAATACAAGAAAATAGTATCATCATGTTATAAGCCTTGGAA

Alignment

ORF - retro_sscr_907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.47 %
• Parental protein coverage: 97.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKAHPPELKKF-MDKKLSLKLNGGRHVQGILR-GFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSII
          ...AHP.E.KK...DKKLSLK...G.HVQGIL..GFDPFMNL.ID.C.EMAT.G..NN..M..I..NSII
Retrocopy VNRAHPAEVKKM>VDKKLSLKSSSG-HVQGILG<GFDPFMNLAIDDCAEMATTG*ENNTKMAIIQENSII

Parental  MLEALE
          ML.ALE
Retrocopy ML*ALE

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	6.90 RPM
SRP014902_testis	0.00 RPM	37.34 RPM
SRP018288_heart	0.00 RPM	19.44 RPM
SRP018288_kidney	0.00 RPM	26.60 RPM
SRP018288_liver	0.16 RPM	22.23 RPM
SRP018288_lung	0.10 RPM	17.00 RPM
SRP018856_adipose	0.00 RPM	28.92 RPM
SRP035408_brain	0.00 RPM	11.85 RPM
SRP035408_liver	0.00 RPM	21.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_907 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 170 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019313	18 retrocopies	retro_cjac_1034, retro_cjac_1227, retro_cjac_1398, retro_cjac_149, retro_cjac_1897, retro_cjac_223, retro_cjac_2419, retro_cjac_2431, retro_cjac_2658, retro_cjac_2795, retro_cjac_3246, retro_cjac_3314, retro_cjac_4078, retro_cjac_547, retro_cjac_763, retro_cjac_796, retro_cjac_897, retro_cjac_998,
Dasypus novemcinctus	ENSDNOG00000019446	18 retrocopies	retro_dnov_1104, retro_dnov_1138, retro_dnov_1150, retro_dnov_1207, retro_dnov_1232, retro_dnov_1297, retro_dnov_221, retro_dnov_2273, retro_dnov_2295, retro_dnov_249, retro_dnov_269, retro_dnov_272, retro_dnov_435, retro_dnov_518, retro_dnov_520, retro_dnov_564, retro_dnov_647, retro_dnov_883,
Felis catus	ENSFCAG00000008118	8 retrocopies	retro_fcat_1006, retro_fcat_1092, retro_fcat_1248, retro_fcat_1467, retro_fcat_1893, retro_fcat_562, retro_fcat_82, retro_fcat_90,
Microcebus murinus	ENSMICG00000015369	10 retrocopies	retro_mmur_1419, retro_mmur_1468, retro_mmur_1550, retro_mmur_265, retro_mmur_395, retro_mmur_59, retro_mmur_595, retro_mmur_625, retro_mmur_735, retro_mmur_901,
Myotis lucifugus	ENSMLUG00000026490	3 retrocopies	retro_mluc_273, retro_mluc_46, retro_mluc_731,
Macaca mulatta	ENSMMUG00000007961	3 retrocopies	retro_mmul_1021, retro_mmul_2048, retro_mmul_300,
Monodelphis domestica	ENSMODG00000011528	1 retrocopy	retro_mdom_1945,
Mustela putorius furo	ENSMPUG00000007221	2 retrocopies	retro_mputfur_100, retro_mputfur_114,
Mus musculus	ENSMUSG00000057278	1 retrocopy	retro_mmus_186,
Nomascus leucogenys	ENSNLEG00000010182	1 retrocopy	retro_nleu_93,
Oryctolagus cuniculus	ENSOCUG00000011214	2 retrocopies	retro_ocun_1032, retro_ocun_57,
Pongo abelii	ENSPPYG00000012324	14 retrocopies	retro_pabe_1054, retro_pabe_1078, retro_pabe_1079, retro_pabe_1169, retro_pabe_1188, retro_pabe_1465, retro_pabe_1603, retro_pabe_1728, retro_pabe_1929, retro_pabe_2041, retro_pabe_2160, retro_pabe_3093, retro_pabe_495, retro_pabe_95,
Rattus norvegicus	ENSRNOG00000016507	1 retrocopy	retro_rnor_409,
Sus scrofa	ENSSSCG00000024776	1 retrocopy	retro_sscr_907 ,
Ictidomys tridecemlineatus	ENSSTOG00000008654	11 retrocopies	retro_itri_1116, retro_itri_1260, retro_itri_128, retro_itri_1395, retro_itri_1871, retro_itri_280, retro_itri_353, retro_itri_572, retro_itri_589, retro_itri_910, retro_itri_947,
Tupaia belangeri	ENSTBEG00000017381	66 retrocopies	retro_tbel_1010, retro_tbel_1076, retro_tbel_1114, retro_tbel_1133, retro_tbel_1161, retro_tbel_1164, retro_tbel_1174, retro_tbel_121, retro_tbel_1288, retro_tbel_1448, retro_tbel_1461, retro_tbel_147, retro_tbel_1478, retro_tbel_149, retro_tbel_164, retro_tbel_1654, retro_tbel_1887, retro_tbel_1939, retro_tbel_1944, retro_tbel_1965, retro_tbel_1966, retro_tbel_1997, retro_tbel_2001, retro_tbel_2143, retro_tbel_217, retro_tbel_236, retro_tbel_239, retro_tbel_241, retro_tbel_2454, retro_tbel_2462, retro_tbel_2572, retro_tbel_2664, retro_tbel_2941, retro_tbel_3098, retro_tbel_3379, retro_tbel_3385, retro_tbel_343, retro_tbel_347, retro_tbel_3495, retro_tbel_3559, retro_tbel_3603, retro_tbel_362, retro_tbel_3699, retro_tbel_3980, retro_tbel_3981, retro_tbel_3983, retro_tbel_4010, retro_tbel_4011, retro_tbel_4177, retro_tbel_4196, retro_tbel_43, retro_tbel_4399, retro_tbel_4442, retro_tbel_4505, retro_tbel_4549, retro_tbel_4609, retro_tbel_465, retro_tbel_489, retro_tbel_697, retro_tbel_726, retro_tbel_736, retro_tbel_805, retro_tbel_921, retro_tbel_93, retro_tbel_936, retro_tbel_947,
Vicugna pacos	ENSVPAG00000007452	10 retrocopies	retro_vpac_182, retro_vpac_196, retro_vpac_25, retro_vpac_290, retro_vpac_295, retro_vpac_352, retro_vpac_42, retro_vpac_59, retro_vpac_591, retro_vpac_641,