RetrogeneDB ID: retro_rnor_348

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:9112368..9113277(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000039876
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000001556
• Aliases: None
• Description: None

Sequence

>retro_rnor_348
ATGGAGAACTCGCAGCTGTGCAAGCTGTTCATCGGCGGCCTGAACGTGCAGACGAGTGAGTCGGGGCTGCGCGGCCACTT
CGAGGCCTTCGGGACGCTGACGGACTGCGTGGTGGTGGTGAACCCCCAGACGAAGCGCTCCCGCTGCTTCGGCTTCGTGA
CCTACTCGAACGTGGAGGAGGCGGACGCCGCCATGGCCGCGTCGCCGCACGCGGTGGACGGCAACACGGTGGAGCTGAAG
CGCGCCGTGTCGCGCGAGGATTCGGCGCGGCCCGGGGCCCACGCCAAGGTGAAGAAGCTGTTCGTGGGCGGCCTCAAGGG
CGACGTGGCGGAGGGCGACCTGATCGAGCACTTCTCGCAGTTCGGCGCCGTGGAGAAGGCGGAGATCATCGCCGACAAGC
AGTCCGGCAAGAAGCGCGGCTTCGGCTTCGTCTACTTCCAGAGCCACGACGCGGCCGACAAGGCGGCGGTGGTCAAGTTC
CACCCGATCCAGGGCCACCGCGTGGAGGTGAAGAAGGCGGTGCCCAAGGAGGATATCCACGCGGGCGGCGGGGGCGCGCG
GGCGGCCCGGGGCGGGCGCGGCGGCGGCCGGGGCCGCGGCGGCGGCGGGGGAGGCGGCGGCGGCCGAGACCAGAACGGGC
TGGCCAAGGGCGGCGGCGGCGGCTACAACAGCTACGGCGGCTACGGGGGCTACGGCGCCTACGGGGGCGGCGGCGGCGGC
GGCTCGTACGGCGGCAGCGACTACGGCAACGGCTTCGGCGGCTTCGGCAGCTACAGCCAGCACCAGTCCTCGTACGGGCC
GATGAAGAGCGGCGGAGGCGGAGGCGGAGGCGGCGGCAGCTGGGGCGGCCGCAGCAACAGTGGACCGTACAGAGGCGGCT
ACGGCGGCGGCGGCGGCGGCGGCTACGGC

Alignment

ORF - retro_rnor_348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 92.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHK
          E..QL.KLFIGGL...T....LR.HFE..GTLTDCVV...PQTKRSR.FGFVTYS.VEE.DAAM.A.PH.
Retrocopy ENSQLCKLFIGGLNVQTSESGLRGHFEAFGTLTDCVVVVNPQTKRSRCFGFVTYSNVEEADAAMAASPHA

Parental  VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGF
          VDG..VE.KRAVSREDS..PGAH..VKK.FVGG.K.D..E..L...F...G..E..E...D.QSGKKRGF
Retrocopy VDGNTVELKRAVSREDSARPGAHAKVKKLFVGGLKGDVAEGDLIEHFSQFGAVEKAEIIADKQSGKKRGF

Parental  AFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQS-AGSQRGRGGGSGNFMGRGGNFGGGGGNFG
          .FV.F..HD..DK..V.K.H.I.GH..EVKKA..K.......G..R...GG.G...GRGG..GGGGG...
Retrocopy GFVYFQSHDAADKAAVVKFHPIQGHRVEVKKAVPKEDIHAGGGGARAARGGRGGGRGRGGGGGGGGGRDQ

Parental  RGGNFGGRGGYGG-GGGGSRGSYGGGDGGYNGFGGDGGN-YGGGPGYSS-RGGYGGGGPGYGNQGGGYGG
          .G...GG.GGY...GG.G..G.YGGG.GG....G.D.GN..GG...YS.....YG....G.G..GGG...
Retrocopy NGLAKGGGGGYNSYGGYGGYGAYGGGGGGGSYGGSDYGNGFGGFGSYSQHQSSYGPMKSGGGGGGGGGSW

Parental  GGGGYDGYNEGGNFGGG
          GG....G...GG..GGG
Retrocopy GGRSNSGPYRGGYGGGG

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	39.33 RPM	66.58 RPM
SRP017611_kidney	24.21 RPM	99.51 RPM
SRP017611_liver	16.88 RPM	58.83 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_348 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF561356	9112566	9112820	100	254	0	254

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348 , retro_rnor_959,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339,
Rattus norvegicus	ENSRNOG00000036839	17 retrocopies	retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,