RetrogeneDB ID: retro_rnor_1763

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:32870176..32870753(-)
• Located in intron of: ENSRNOG00000000555

Retrocopy information

• Ensembl ID: ENSRNOG00000000554
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Csrp2
• Ensembl ID: ENSRNOG00000003772
• Aliases: Csrp2, SmLIM
• Description: cysteine and glycine-rich protein 2 [Source:RefSeq peptide;Acc:NP_803174]

Sequence

>retro_rnor_1763
ATGCCTGTCTGGGGCAGTGGAAATAAGTGCGGGGCCTGCGGGAGAACGGTGTACCATGCTGAAGAGGTGCAGTGTGACGG
GCGGAGCTTCCACCGGTGCTGCTTTCTGTGCATGGTTTGCAGGAAATATTTAGACAGCACAACAGTGGCAATTCATGATG
AAGAGATCTACTGCAAATCATGCTACGGAAAGAAGTATGGACCAAAAGGCTATGGTTATGGCCAGGGCGCTGGCACGCTC
AACATGGGCCGTCGTGAGAAGCTGGGTATCAAGCCAGAGAGTGCTCAACCTCACAGGCCTACAACAAACCCAAACACTTC
TAAATTTGCCCAGAAATATGGAGGTGCTGAGAAGTGTTCCAGGTGTGGGGATTCTGTGTATGCTGCTGAGAAGATCATTA
GAGCTGGAAAGCCCTGGCACAAAAACTTTCCGATGTGCCAAGTGTGGGAAGAGTCTGGAGTCTACAACTCTGACTGAGAA
GGAAGGTGAAATCTACTGTAAAGGGTGCTACTCAAAGAACTTTGGGCCCAAGGGATTCGGCTATGGTCAAGGAGCAGGGG
CCCTTGTTCATGCTCAG

Alignment

ORF - retro_rnor_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSCYGKKYGPKG
          MPVWG.GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRK.LDSTTVAIHDEEIYCKSCYGKKYGPKG
Retrocopy MPVWGSGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKYLDSTTVAIHDEEIYCKSCYGKKYGPKG

Parental  YGYGQGAGTLNMDRGERLGIKPESAQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGK-PW
          YGYGQGAGTLNM.R.E.LGIKPESAQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKII.AGK.P.
Retrocopy YGYGQGAGTLNMGRREKLGIKPESAQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIRAGK>PG

Parental  HKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGFGYGQGAGALVHAQ
          .K..FRCAKCGKSLESTTLTEKEGEIYCKGCY.KNFGPKGFGYGQGAGALVHAQ
Retrocopy TKT-FRCAKCGKSLESTTLTEKEGEIYCKGCYSKNFGPKGFGYGQGAGALVHAQ

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	5.97 RPM
SRP017611_kidney	0.07 RPM	77.81 RPM
SRP017611_liver	0.13 RPM	2.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1763 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1763 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019153	6 retrocopies	retro_cjac_1266, retro_cjac_1285, retro_cjac_1384, retro_cjac_1555, retro_cjac_2919, retro_cjac_3150,
Equus caballus	ENSECAG00000015606	1 retrocopy	retro_ecab_412,
Echinops telfairi	ENSETEG00000019648	1 retrocopy	retro_etel_1589,
Homo sapiens	ENSG00000175183	2 retrocopies	retro_hsap_2833, retro_hsap_2836,
Gorilla gorilla	ENSGGOG00000026601	2 retrocopies	retro_ggor_1967, retro_ggor_1969,
Myotis lucifugus	ENSMLUG00000002384	3 retrocopies	retro_mluc_1888, retro_mluc_486, retro_mluc_720,
Macaca mulatta	ENSMMUG00000018257	1 retrocopy	retro_mmul_1474,
Mustela putorius furo	ENSMPUG00000017469	1 retrocopy	retro_mputfur_262,
Nomascus leucogenys	ENSNLEG00000004885	2 retrocopies	retro_nleu_1208, retro_nleu_1592,
Oryctolagus cuniculus	ENSOCUG00000008330	2 retrocopies	retro_ocun_1165, retro_ocun_649,
Otolemur garnettii	ENSOGAG00000013999	6 retrocopies	retro_ogar_1220, retro_ogar_1411, retro_ogar_1688, retro_ogar_2589, retro_ogar_2909, retro_ogar_3399,
Ochotona princeps	ENSOPRG00000011987	1 retrocopy	retro_opri_1125,
Pongo abelii	ENSPPYG00000004790	2 retrocopies	retro_pabe_2199, retro_pabe_2347,
Rattus norvegicus	ENSRNOG00000003772	1 retrocopy	retro_rnor_1763 ,
Rattus norvegicus	ENSRNOG00000005041	2 retrocopies	retro_rnor_141, retro_rnor_2541,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sorex araneus	ENSSARG00000002290	1 retrocopy	retro_sara_526,
Ictidomys tridecemlineatus	ENSSTOG00000010876	1 retrocopy	retro_itri_551,
Tupaia belangeri	ENSTBEG00000009767	3 retrocopies	retro_tbel_1866, retro_tbel_4404, retro_tbel_4407,
Tursiops truncatus	ENSTTRG00000014596	1 retrocopy	retro_ttru_1332,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,