RetrogeneDB ID: retro_sscr_40

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL896504.1:7608..8184(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000022917
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAC2
• Ensembl ID: ENSSSCG00000021944
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Source:HGNC Symbol;Acc:9802]

Sequence

>retro_sscr_40
ATGCAGACGATCAAATGTGTGGTTGTGGGGGATGGGGCTGTAGGTAAGACCTGTCTCCTCATCAGTTACACCACAAATGC
CTTTCCTGAGGAGTATATCCCCACTGTGTTTGACAACTATAGTGCCCAGACATCGGTGGATGGCCAAATCGTCAGCCTGA
ATCTGTGGGACACAGCTGGCCAAGAGGAGTATGACCGACTGCGAACGCTGTCCTACCCCCAGACTAATATCTTTGTCATT
TGTTTTTCCATTGGCAACCCATCCTCTTATGCCAACGTGAGGCATAAGTGGTACCCAGAGGTCTCGCATCATTGCCCCAA
TGTACCCGTTTTGCTGGTAGGCACCAAGAGGGACCTGCGGAGTGACCTTGAGACAGTGAAGAAGCTGAAGGAACAGAGCC
TAGTGCCCACAACTCCTCAGCAAGGCACTTCCCTGGCTAAGCAGGTGGGGGCTGTGAAGTATCTGGAATGTTCGGCCCTG
ATGCAGGATGGGGTCCATGAGGTATTTTCAGAAGCTGTCCGGGCTGTGCTTTACCCTGCCACAAAGAAGAACACCAAGAA
GTGTGTCCTCTTATAG

Alignment

ORF - retro_sscr_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRPL
          MQ.IKCVVVGDGAVGKTCLLISYTTNAFP.EYIPTVFDNYSA...VD...V.L.LWDTAGQE.YDRLR.L
Retrocopy MQTIKCVVVGDGAVGKTCLLISYTTNAFPEEYIPTVFDNYSAQTSVDGQIVSLNLWDTAGQEEYDRLRTL

Parental  SYPQTDVFLICFSLVSPASYENVRAKWFPEVRHHCPSTPIILVGTKLDLRDDKDTIEKLKEKKLAPITYP
          SYPQT..F.ICFS...P.SY.NVR.KW.PEV.HHCP..P..LVGTK.DLR.D..T..KLKE..L.P.T..
Retrocopy SYPQTNIFVICFSIGNPSSYANVRHKWYPEVSHHCPNVPVLLVGTKRDLRSDLETVKKLKEQSLVPTTPQ

Parental  QGLALAKEIDSVKYLECSALTQRGLKTVFDEAIRAVLCPQPTRPQKRPCSIL
          QG..LAK....VKYLECSAL.Q.G...VF.EA.RAVL.P..T......C..L
Retrocopy QGTSLAKQVGAVKYLECSALMQDGVHEVFSEAVRAVLYP-ATKKNTKKCVLL

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	1.33 RPM
SRP014902_testis	0.14 RPM	17.54 RPM
SRP018288_heart	0.00 RPM	6.31 RPM
SRP018288_kidney	0.00 RPM	10.64 RPM
SRP018288_liver	0.00 RPM	11.03 RPM
SRP018288_lung	0.00 RPM	156.61 RPM
SRP018856_adipose	0.00 RPM	17.25 RPM
SRP035408_brain	0.00 RPM	1.30 RPM
SRP035408_liver	0.00 RPM	4.70 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_40 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_40 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009889	2 retrocopies	retro_amel_1691, retro_amel_647,
Callithrix jacchus	ENSCJAG00000002144	4 retrocopies	retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Equus caballus	ENSECAG00000022570	2 retrocopies	retro_ecab_619, retro_ecab_705,
Erinaceus europaeus	ENSEEUG00000009509	1 retrocopy	retro_eeur_20,
Felis catus	ENSFCAG00000025776	2 retrocopies	retro_fcat_1064, retro_fcat_826,
Gorilla gorilla	ENSGGOG00000010612	2 retrocopies	retro_ggor_1403, retro_ggor_188,
Loxodonta africana	ENSLAFG00000013012	1 retrocopy	retro_lafr_117,
Macropus eugenii	ENSMEUG00000012295	2 retrocopies	retro_meug_252, retro_meug_552,
Microcebus murinus	ENSMICG00000017775	4 retrocopies	retro_mmur_1104, retro_mmur_1557, retro_mmur_20, retro_mmur_600,
Myotis lucifugus	ENSMLUG00000012668	2 retrocopies	retro_mluc_326, retro_mluc_860,
Macaca mulatta	ENSMMUG00000018854	2 retrocopies	retro_mmul_1346, retro_mmul_210,
Mustela putorius furo	ENSMPUG00000012682	2 retrocopies	retro_mputfur_872, retro_mputfur_911,
Nomascus leucogenys	ENSNLEG00000014759	7 retrocopies	retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus	ENSOCUG00000016115	1 retrocopy	retro_ocun_43,
Otolemur garnettii	ENSOGAG00000004138	1 retrocopy	retro_ogar_2977,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pteropus vampyrus	ENSPVAG00000002281	2 retrocopies	retro_pvam_21, retro_pvam_609,
Sarcophilus harrisii	ENSSHAG00000014852	1 retrocopy	retro_shar_763,
Sus scrofa	ENSSSCG00000003520	1 retrocopy	retro_sscr_899,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Sus scrofa	ENSSSCG00000021944	4 retrocopies	retro_sscr_40 , retro_sscr_565, retro_sscr_582, retro_sscr_882,
Ictidomys tridecemlineatus	ENSSTOG00000023766	1 retrocopy	retro_itri_510,
Tursiops truncatus	ENSTTRG00000001099	8 retrocopies	retro_ttru_1029, retro_ttru_1065, retro_ttru_1188, retro_ttru_1599, retro_ttru_1904, retro_ttru_318, retro_ttru_379, retro_ttru_825,