RetrogeneDB ID: retro_rnor_2168

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:114690016..114690695(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Spcs2
• Ensembl ID: ENSRNOG00000018164
• Aliases: Spcs2, RGD1311253
• Description: signal peptidase complex subunit 2 homolog [Source:RefSeq peptide;Acc:NP_001178530]

Sequence

>retro_rnor_2168
ATGGAAGAGGTGGTGTCTCGGGATGGGTGAAACAGTGGTGGCAGAGGCAGTAGTGGGCCTGGCGGTGTCCCAGCTGAGGG
ACAGTCAGCAGTCTCAGTGGTTTGTTGGGTAAGTGAATAATTGATAATGATCCCTGTATTAATTGGGATGTAAAAAAGTG
AGATGGATCAGCTGTGAAAAACTCTCTGGATGATTCTGCCAAAAGGGTATTCCTGCAAAAGTACAAGTACGTGGAGAACT
TTGATCCTATTGAAGGTCGCCTTACCATCTCTACCATCCCCTGCTTCTTTGCCATACTGGCTTTGATCTGGGATTACATG
CATCCTTTCCAGAGTCCGAGCCAGTTTTGGCATTGCGTGTCATAGTCCTATTTCTTGATGATGGGCTGACCATTCATCCC
TCAGATAAAGAGAAGAGCATCTTCCTAGTGGTCCACAGAAGAGACCCTAGAGGAAGGGATCCTGATGATCTTTGGCAGCT
GCCATCCAGCCTCAAAAGGTTCAATGACAAATACACCCTGAAGTTGACCTCCATCAGTGGGAGGACAATGCAGCAGCTGG
AAGCCAAGTTCACCAAGTCCATTGCTAAGTAGTTTTACCACAGCGGGACATTGACCATAGATGCATATGAATCTGAAATA
TCCAGGCTCCATGACAGTCTCATCACAGAAAGAAAAATA

Alignment

ORF - retro_rnor_2168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAASQGGRSGGGGGSSGPGGGP-SCGTSSSRSGLLDKWKIDDKPV---KIDKWDGSAVKNSLDDSAKK
          M....S..G...GG.GSSGPGG.P.S.GT.SS.SGLL.K..ID..P.......K.DGSAVKNSLDDSAK.
Retrocopy MEEVVSRDG*NSGGRGSSGPGGVP<S*GTVSSLSGLLGK*IIDNDPCINWDVKK*DGSAVKNSLDDSAKR

Parental  VLLEKYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPF-PESKPVLALCVVSYFVMMGILTIYTSYK
          V.L.KYKYVENF..I.GRLTI.TI.CFFAI.ALIWDYMHPF.PES.PVLAL.V...F...G.LTI..S.K
Retrocopy VFLQKYKYVENFDPIEGRLTISTIPCFFAILALIWDYMHPF<PESEPVLALRVIVLFLDDG-LTIHPSDK

Parental  EKSIFLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVM
          EKSIFLV.HR.DP.G.DPDD.WQL.SSLKRF.DKYTLKLT.ISGRT.QQ.EA.FTKSIAK.F.HSGTL..
Retrocopy EKSIFLVVHRRDPRGRDPDDLWQLPSSLKRFNDKYTLKLTSISGRTMQQLEAKFTKSIAK*FYHSGTLTI

Parental  DAYEPEISRLHDSLATERKI
          DAYE.EISRLHDSL.TERKI
Retrocopy DAYESEISRLHDSLITERKI

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	60.32 RPM
SRP017611_kidney	0.00 RPM	54.99 RPM
SRP017611_liver	0.00 RPM	55.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2168 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2168 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017127	1 retrocopy	retro_amel_1372,
Choloepus hoffmanni	ENSCHOG00000002974	3 retrocopies	retro_chof_1392, retro_chof_1588, retro_chof_2300,
Callithrix jacchus	ENSCJAG00000015576	2 retrocopies	retro_cjac_1500, retro_cjac_1929,
Cavia porcellus	ENSCPOG00000007273	2 retrocopies	retro_cpor_438, retro_cpor_578,
Dipodomys ordii	ENSDORG00000009679	1 retrocopy	retro_dord_423,
Homo sapiens	ENSG00000118363	4 retrocopies	retro_hsap_1488, retro_hsap_3137, retro_hsap_360, retro_hsap_723,
Gorilla gorilla	ENSGGOG00000014500	3 retrocopies	retro_ggor_1141, retro_ggor_372, retro_ggor_610,
Microcebus murinus	ENSMICG00000011153	2 retrocopies	retro_mmur_1566, retro_mmur_656,
Macaca mulatta	ENSMMUG00000010685	1 retrocopy	retro_mmul_26,
Monodelphis domestica	ENSMODG00000007130	2 retrocopies	retro_mdom_1127, retro_mdom_1454,
Mus musculus	ENSMUSG00000035227	1 retrocopy	retro_mmus_2088,
Nomascus leucogenys	ENSNLEG00000016949	2 retrocopies	retro_nleu_1710, retro_nleu_470,
Otolemur garnettii	ENSOGAG00000015621	1 retrocopy	retro_ogar_2649,
Ochotona princeps	ENSOPRG00000014459	2 retrocopies	retro_opri_266, retro_opri_948,
Pongo abelii	ENSPPYG00000003682	4 retrocopies	retro_pabe_1237, retro_pabe_2619, retro_pabe_2817, retro_pabe_625,
Pan troglodytes	ENSPTRG00000004073	1 retrocopy	retro_ptro_1007,
Rattus norvegicus	ENSRNOG00000018164	2 retrocopies	retro_rnor_2078, retro_rnor_2168 ,
Sarcophilus harrisii	ENSSHAG00000005389	1 retrocopy	retro_shar_787,
Sus scrofa	ENSSSCG00000014850	1 retrocopy	retro_sscr_648,
Ictidomys tridecemlineatus	ENSSTOG00000012647	2 retrocopies	retro_itri_1283, retro_itri_1584,
Tursiops truncatus	ENSTTRG00000005830	3 retrocopies	retro_ttru_1478, retro_ttru_1496, retro_ttru_1867,