RetrogeneDB ID: retro_mmus_1819

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:22441134..22441914(+)
• Located in intron of: ENSMUSG00000052387

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nsa2
• Ensembl ID: ENSMUSG00000060739
• Aliases: Nsa2, 5730427N09Rik, LNR42, Nsa2p, Tinp1, Yr29
• Description: NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913883]

Sequence

>retro_mmus_1819
ATGCCACAAAATGAATATATTGAATTGCACCGCAAACGATACGGATATCGTTTGGACTACCATGAGAAAAAGAGAAAGAA
AGAAGGTCGGGAGGCCCATGAACGTTCAAAGAAGGCAAAAAAAATGATTGGCCTGAAGGCTAAGCTCTACCATAAACAGC
GCCATGCCGAGAAAATACAAATGAAAAAGACTATTAAGATGCATGAGAAGAGAAACACCAAGCAGAAGGATGATGAGAAG
ACGCCGCAGGGAGCAGTCCCCGCCTATCTGCTGGACAGAGAGGGCCAGTCGAGAGCAAAAGTCCTTTCTAACATGATTAA
GCAGAAACGGAAAGAAAAGGCGGGAAAATGGGAGGTCCCTCTACCCAAAGTTCGTGCCCAAGGAGAAACAGAAGTATTGA
AAGTTATTCGGACAGGAAAAAGGAAAAAAAAGGCATGGAAGAGAATGGTTACTAAAGTCTGCTTTGTTGGTGATGGCTTT
ACAAGAAAACCACCGAAATATGAAAGGTTCATTAGGCCTATGGGTCTACGTTTCAAAAAAGCCCATGTCACACACCCTGA
GCTGAAAGCTACCTTTTGCCTGCCTATTCTCGGTGTGAAAAAGAATCCATCGTCCCCATTATATACAACCCTGGGTGTGA
TCACCAAAGGTACAGTTATTGAAGTGAATGTGAGCAAGCTGGGCCTTGTGACACAAGGAGGCAAGGTGATTTGGGGAAAG
TACGCCCAAGTTACCAACAATCCTGAGAACGATGGGTGCATAAATGCGGTCTTGCTGGTC

Alignment

ORF - retro_mmus_1819 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQNEYIELHRKRYGYRLDYHEKKRKKEGREAHERSKKAKKMIGLKAKLYHKQRHAEKIQMKKTIKMHEK
          MPQNEYIELHRKRYGYRLDYHEKKRKKEGREAHERSKK....IGLKAKLYHKQRHAEKIQMKKTIKMHEK
Retrocopy MPQNEYIELHRKRYGYRLDYHEKKRKKEGREAHERSKKXXXXIGLKAKLYHKQRHAEKIQMKKTIKMHEK

Parental  RNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRTGK
          RNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRT..
Retrocopy RNTKQKDDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRTXX

Parental  RKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYTT
          ....AWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYTT
Retrocopy XXXXAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYTT

Parental  LGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV
          LGVITKGTVIEVNVS.LGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV
Retrocopy LGVITKGTVIEVNVSKLGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV

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
SRP007412_brain	0.05 RPM	10.05 RPM
SRP007412_cerebellum	0.04 RPM	9.99 RPM
SRP007412_heart	0.12 RPM	16.09 RPM
SRP007412_kidney	0.02 RPM	22.87 RPM
SRP007412_liver	0.03 RPM	19.72 RPM
SRP007412_testis	0.05 RPM	25.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1819 was not detected

EST

2 EST(s) were mapped to retro_mmus_1819 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV105732	22441418	22441545	99.3	126	1	125
AV508710	22441335	22441565	98.3	225	3	220

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_63047	277 libraries	153 libraries	59 libraries	94 libraries	489 libraries

The graphical summary, for retro_mmus_1819 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1819 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003066	3 retrocopies	retro_btau_326, retro_btau_931, retro_btau_949,
Canis familiaris	ENSCAFG00000008311	4 retrocopies	retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Callithrix jacchus	ENSCJAG00000016874	1 retrocopy	retro_cjac_116,
Equus caballus	ENSECAG00000005528	1 retrocopy	retro_ecab_445,
Echinops telfairi	ENSETEG00000004095	13 retrocopies	retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus	ENSFCAG00000011978	1 retrocopy	retro_fcat_98,
Loxodonta africana	ENSLAFG00000009910	4 retrocopies	retro_lafr_253, retro_lafr_455, retro_lafr_620, retro_lafr_714,
Macropus eugenii	ENSMEUG00000015798	3 retrocopies	retro_meug_1191, retro_meug_1408, retro_meug_161,
Myotis lucifugus	ENSMLUG00000014464	4 retrocopies	retro_mluc_1596, retro_mluc_1664, retro_mluc_757, retro_mluc_917,
Monodelphis domestica	ENSMODG00000001900	4 retrocopies	retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mus musculus	ENSMUSG00000060739	25 retrocopies	retro_mmus_1121, retro_mmus_1329, retro_mmus_1472, retro_mmus_1558, retro_mmus_1587, retro_mmus_1751, retro_mmus_1785, retro_mmus_1819 , retro_mmus_1890, retro_mmus_2426, retro_mmus_2617, retro_mmus_2706, retro_mmus_2806, retro_mmus_3105, retro_mmus_3246, retro_mmus_3302, retro_mmus_3340, retro_mmus_3485, retro_mmus_3671, retro_mmus_3713, retro_mmus_402, retro_mmus_518, retro_mmus_674, retro_mmus_690, retro_mmus_890,
Oryctolagus cuniculus	ENSOCUG00000006536	6 retrocopies	retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Pteropus vampyrus	ENSPVAG00000005396	2 retrocopies	retro_pvam_1352, retro_pvam_476,
Rattus norvegicus	ENSRNOG00000016530	15 retrocopies	retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus	ENSSARG00000009424	4 retrocopies	retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Sus scrofa	ENSSSCG00000014075	2 retrocopies	retro_sscr_287, retro_sscr_288,
Tupaia belangeri	ENSTBEG00000012978	56 retrocopies	retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,