RetrogeneDB ID: retro_rnor_1282

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:88136459..88137533(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3bp1
• Ensembl ID: ENSRNOG00000013186
• Aliases: G3bp1, G3bp, RGD1310666
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:RefSeq peptide;Acc:NP_598249]

Sequence

>retro_rnor_1282
ATGGTTATGGAGAAGCCTAGTCCCCTGCCAGTTGGGCGGGAATTTGTGCGACAGTACTACACCCTGCTGATCCAGGCCAC
GGACATGCTGCACAGATTTTAAGGAAAGAGCTTTTCCTATGCCCACGGGGGCTTGGATTCCAATGGGAAGCCAGCAGATG
CAATCTTCCTGTAGAAGGAAATCCACAGGAAAGTGATATCACAAAACCTCACCAAGTGCCACTCCAACATCCGCCATGTG
GAGGCTCACGCAATTCTGAATGAGGGGGTGGTGGTCCAGGTGATGGGGCTACTGTCCAACAACAGCCAAGCTCTGAGGAG
GTTCATGCAGACCTTGGCCCTTGTTCCTAAGGGCTCTGTTGCCAACAAAGTCTAGGTTCACAACGATATCATCAGATACC
AAGATGAGATCTTCCGTGGCTTTGTCACAGAGCCTCAAGAGGAATCCAAGGAAGTAGAGGGACCCGAAGAAAGACAGCAA
ACACCTGAGGTGGTGCCTGATGATTCTGGAACTTTCTATGATCAGACTGTCAGCAATGACTTGGAGGATCATTTAGAGGA
ACCGGTTGTGGAACCGGAACTGGAACTGGAACCAGACGCGGAGCCAGAACCTGCTGTTCAAGAGATCAAGCCCGAGCCTG
CATTGGAAGAAGCCGCTCCTGAGGATGTGCAGAAGAGCGCTTCCCTGGTTCCGGAAGAGGCAGCCCCGGAAGACGTGGCC
CCAACATAGGAGGACATGAGGACATTTTCTTGGGCACCTGTGACTACTAAGAAGTTTCCTCCCAGTGGGGCTGTTCCAGT
GACGCGACACCACCTCATGTGGTCAAAGTGCCGGCACCACAGCCACGGCAGAATGCCTGACTCTCAGATCCCACCACAAA
GGCCTCAGAGAGATCAGAGAGTTCAAGAGCAGCAGATCAATATCCCTCCTCAGCGAGGACCCTGACCAGTCCGTGAGGCT
GGTGAACCAGGAGATGTGGAACCTTGAAGGATGGTGAGGCACCTTGACGGTCACCAGCTCTTCACTGGGAACCTGCCACA
TGAGGTTGACAAGTCGGAACCAAAGCATTATTTT

Alignment

ORF - retro_rnor_1282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 76.99 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYAHGGLDSNGKPADAVYGQKEIHRKVMSQNF
          MVMEKPSPL.VGREFVRQYYTLL.QA.DMLHRF.GK..SYAHGGLDSNGKPADA....KEIHRKV.SQN.
Retrocopy MVMEKPSPLPVGREFVRQYYTLLIQATDMLHRF*GKSFSYAHGGLDSNGKPADAIFL*KEIHRKVISQNL

Parental  TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGG
          T.CH..IRHV.AHA.LN.GVVVQVMGLLSNN.QALRRFMQT..L.P.GSVANK..VHNDI.RYQDE.F.G
Retrocopy TKCHSNIRHVEAHAILNEGVVVQVMGLLSNNSQALRRFMQTLALVPKGSVANKV*VHNDIIRYQDEIFRG

Parental  FVTEPQEESEEEVEEPEERQQSPEVVADDSGTFYDQTVSNDLEEHLEEPVVEPEPEPEPEPEPEPVSDIQ
          FVTEPQEES.E.VE.PEERQQ.PEVV.DDSGTFYDQTVSNDLE.HLEEPV...........EPEP.....
Retrocopy FVTEPQEESKE-VEGPEERQQTPEVVPDDSGTFYDQTVSNDLEDHLEEPVXXXXXXXXXDAEPEPAVQEI

Parental  EDKP---EPALEEAAPEDVQKSASPAPADVAPAQEDLRTFSWASVTSKNLPPSGAVPVT-GTPPHVVKVP
          ...P...E.A.E.............AP.DVAP..ED.RTFSWA.VT.K..PPSGAVPVT..TPPHVVKVP
Retrocopy KPEPALEEAAPEDVQKSASLVPEEAAPEDVAPT*EDMRTFSWAPVTTKKFPPSGAVPVT<ATPPHVVKVP

Parental  ASQPRPESK-PDSQIPPQRPQRDQRAREQRINIPPQRGPRPIREAGEPGDVEPRRMVRHPDSHQLFIGNL
          A..P.P....PDSQIPPQRPQRDQR..EQ.INIPPQRGP.P.REAGEPGDVEP.RMVRH.D.HQLF.GNL
Retrocopy A--PQPRQN>PDSQIPPQRPQRDQRVQEQQINIPPQRGP*PVREAGEPGDVEP*RMVRHLDGHQLFTGNL

Parental  PHEVDKSELKDFF
          PHEVDKSE.K..F
Retrocopy PHEVDKSEPKHYF

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
SRP017611_brain	0.00 RPM	98.71 RPM
SRP017611_kidney	0.00 RPM	116.96 RPM
SRP017611_liver	0.20 RPM	61.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1282 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1282 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Mus musculus	ENSMUSG00000018583	3 retrocopies	retro_mmus_1389, retro_mmus_3229, retro_mmus_3688,
Nomascus leucogenys	ENSNLEG00000016470	1 retrocopy	retro_nleu_1814,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282 ,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460, retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,