RetrogeneDB ID: retro_rnor_2297

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:72951460..72951896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ostc
• Ensembl ID: ENSRNOG00000023322
• Aliases: Ostc, Dc2, RGD1560708
• Description: Oligosaccharyltransferase complex subunit OSTC [Source:UniProtKB/Swiss-Prot;Acc:B0K025]

Sequence

>retro_rnor_2297
CTCTACTGAGTCCCATTTTTAATGCTTGAATGCCTCAACCTGAAGCTGAAGAAACTGCCCTGGGGGCACATGGCTGTCAG
CTATGATGGTGTATGCCCTGATGGTGGTATCTTACTTCTTATTACCAGAAGAATAATCTATGATGTTATCGTTGAACCTC
CAAGTATTGGATCAATGAGTGATGAACATGGTCATCAGAGACTAGTAGCTTTCTTGGCTTACAGAGTAAACGGACAGTAT
AATATGGAAGGACTTGCATCTAGTTTTATGTTAACAATGGGAGGTTTAGGTTTCATAATCCTGGACTGATCAATGCACCA
AGTATACCAAAACTCAATAGGTTTATTCTTCTTTTCATTAGCTTTGTCTGCATTCTATTGAGTTTCTTCATGGCTAGGTA
TTCATGAGAATGAAATTGCTAGGGTACTTGATGGGC

Alignment

ORF - retro_rnor_2297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.67 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LYRVPFLVLECPNLKLKKPPWVHMP-SAMTVYALVVVSYFL-ITGGIIYDVIVEPPSVGSMTDEHGHQRP
          LY.VPFL.LEC.NLKLKK.PW.HM..SAM.VYAL.VVSYFL.IT..IIYDVIVEPPS.GSM.DEHGHQR.
Retrocopy LY*VPFLMLECLNLKLKKLPWGHMA>SAMMVYALMVVSYFL<ITRRIIYDVIVEPPSIGSMSDEHGHQRL

Parental  VAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRS-NAPNIPKLNRFLLLFIGFVCVLLSFFMAR-VFM
          VAFLAYRVNGQY.MEGLASSF..TMGGLGFIILD.S.NAP.IPKLNRF.LLFI.FVC.LLSFFMAR.VFM
Retrocopy VAFLAYRVNGQYNMEGLASSFMLTMGGLGFIILD*S<NAPSIPKLNRFILLFISFVCILLSFFMAR<VFM

Parental  RMKLPGYLMG
          RMKL.GYLMG
Retrocopy RMKLLGYLMG

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	15.24 RPM
SRP017611_kidney	0.00 RPM	26.45 RPM
SRP017611_liver	0.00 RPM	34.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2297 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2297 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297, retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297 ,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,