RetrogeneDB ID: retro_rnor_1831

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:145262170..145262715(+)
• Located in intron of: ENSRNOG00000008746

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gnb2l1
• Ensembl ID: ENSRNOG00000002390
• Aliases: Gnb2l1, RACK1
• Description: Guanine nucleotide-binding protein subunit beta-2-like 1 [Source:UniProtKB/Swiss-Prot;Acc:P63245]

Sequence

>retro_rnor_1831
CACTCCCACTTTGTTATCTATGATGTTATCTCCTCTGATGGTCAATTTGCCCTCTCAGGCCTTTGGGATGGAACACTGTG
CCTCTGGGATCTCACTACGGGCACTACCACGAGACAATTTGTCGGCCATACCAAGGATGTGCTCGAGTGTGGCCTTCTCT
GAAAACTGGCAGATTGTCTCTGGGTACCGAGGCAAGACCATAAAGTTATAGAATATTCTGGGTGTCTGCAAATACACTGT
CCAGGATTAGAGTCATTCAGGATGGGTGTCTTGTGTCCACTTCTCCCCAAACAACAGCAACCCTATCATCGTCTCCTGTG
GATGGGACGAGCTGGTCAAGGTGTGGAATCTGGCTAACTGCAAGCTAAAGACCAACCACATTGGCCACATGGCTATCTGA
GCACAGAAACCGTCTCTCTAGATGGATCCCTTTGTGCTTCTGGAGGCCAGGATGACCAGGCTATGCTGTGGGACCTCAGT
GAAGGCAAGCACCTTTACACTTTAGATGGCCAGACATCATCAATTCCTTGTGCTTCAGCCCTAAC

Alignment

ORF - retro_rnor_1831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVL-SVAFSSDNRQIVSGSRDKTIK
          HSHFV...VISSDGQFALSG.WDGTL.LWDLTTGTTTR.FVGHTKDVL.SVAFS..N.QIVSG.R.KTIK
Retrocopy HSHFVIYDVISSDGQFALSGLWDGTLCLWDLTTGTTTRQFVGHTKDVL>SVAFS-ENWQIVSGYRGKTIK

Parental  LWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHT-GYLNTVT
          L.N.LGVCKYTVQD.SHS.WVSCV.FSPN.SNPIIVSCGWD.LVKVWNLANCKLKTNHIGH..GYL.T.T
Retrocopy L*NILGVCKYTVQD*SHSGWVSCVHFSPNNSNPIIVSCGWDELVKVWNLANCKLKTNHIGHM<GYLSTET

Parental  VSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDG-GDIINALCFSPN
          VS.DGSLCASGG.D.QAMLWDL.EGKHLYTLDG..DIIN.LCFSPN
Retrocopy VSLDGSLCASGGQDDQAMLWDLSEGKHLYTLDG<PDIINSLCFSPN

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	93.68 RPM
SRP017611_kidney	0.07 RPM	195.25 RPM
SRP017611_liver	0.00 RPM	103.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1831 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1831 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012008	1 retrocopy	retro_acar_185,
Ailuropoda melanoleuca	ENSAMEG00000000004	1 retrocopy	retro_amel_1627,
Bos taurus	ENSBTAG00000019648	1 retrocopy	retro_btau_1461,
Canis familiaris	ENSCAFG00000024818	1 retrocopy	retro_cfam_1824,
Callithrix jacchus	ENSCJAG00000018752	1 retrocopy	retro_cjac_2876,
Cavia porcellus	ENSCPOG00000008724	1 retrocopy	retro_cpor_687,
Dipodomys ordii	ENSDORG00000010735	1 retrocopy	retro_dord_117,
Equus caballus	ENSECAG00000022567	3 retrocopies	retro_ecab_172, retro_ecab_218, retro_ecab_986,
Erinaceus europaeus	ENSEEUG00000008729	1 retrocopy	retro_eeur_368,
Echinops telfairi	ENSETEG00000016024	3 retrocopies	retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens	ENSG00000204628	1 retrocopy	retro_hsap_3226,
Gorilla gorilla	ENSGGOG00000025367	1 retrocopy	retro_ggor_2194,
Macropus eugenii	ENSMEUG00000011055	3 retrocopies	retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus	ENSMLUG00000015507	1 retrocopy	retro_mluc_811,
Macaca mulatta	ENSMMUG00000003604	1 retrocopy	retro_mmul_1956,
Monodelphis domestica	ENSMODG00000004091	1 retrocopy	retro_mdom_1426,
Mustela putorius furo	ENSMPUG00000001148	2 retrocopies	retro_mputfur_1103, retro_mputfur_1111,
Mus musculus	ENSMUSG00000020372	1 retrocopy	retro_mmus_3282,
Nomascus leucogenys	ENSNLEG00000002604	1 retrocopy	retro_nleu_729,
Ornithorhynchus anatinus	ENSOANG00000002600	1 retrocopy	retro_oana_127,
Otolemur garnettii	ENSOGAG00000014924	2 retrocopies	retro_ogar_1257, retro_ogar_1591,
Pongo abelii	ENSPPYG00000019939	1 retrocopy	retro_pabe_149,
Pan troglodytes	ENSPTRG00000022734	1 retrocopy	retro_ptro_2178,
Rattus norvegicus	ENSRNOG00000002390	3 retrocopies	retro_rnor_1831 , retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus	ENSSTOG00000007063	1 retrocopy	retro_itri_1752,
Tupaia belangeri	ENSTBEG00000014661	2 retrocopies	retro_tbel_3897, retro_tbel_3899,