RetrogeneDB ID: retro_mmus_342

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:86473658..86474003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl30
• Ensembl ID: ENSMUSG00000058600
• Aliases: None
• Description: ribosomal protein L30 [Source:MGI Symbol;Acc:MGI:98037]

Sequence

>retro_mmus_342
ATGGTGGCCACAAAGAAGATGAAAGAGTCTCTGGAGTCGATCAACTCTAGGCTCCAGTTTGTTATGAAAAGTGGAAAGTA
CTTGCGGGAGTTCAAACAGACTCTGAAGATGGTCAGACAAGGCAAAGCAAAGTTGGTTATCCTCGCCGACAGCTGCCCAG
CTTGGAGGAAATCTGAAATAGAATACTATGCCATGTTGGCTAAAACTGGGGTCCATCACTACAGAGGCAATAATATGAAA
TTGGGTACAGCATGTGGAAAATACTACAGAGTTTGCACACTGGCTAGCATCGACCCAAGTGATTCTGATATTATTAGAAG
CATGCCAGAAGACACTGGTGAGAAG

Alignment

ORF - retro_mmus_342 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTG
          MVA.KK.K.SLESINSRLQ.VMKSGKY....KQTLKM.RQGKAKLVILA..CPA.RKSEIEYYAMLAKTG
Retrocopy MVATKKMKESLESINSRLQFVMKSGKYLREFKQTLKMVRQGKAKLVILADSCPAWRKSEIEYYAMLAKTG

Parental  VHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK
          VHHY.GNN..LGTACGKYYRVCTLA.IDP.DSDIIRSMPE.TGEK
Retrocopy VHHYRGNNMKLGTACGKYYRVCTLASIDPSDSDIIRSMPEDTGEK

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	0.00 RPM	46.73 RPM
SRP007412_cerebellum	0.00 RPM	28.92 RPM
SRP007412_heart	0.00 RPM	78.98 RPM
SRP007412_kidney	0.00 RPM	55.54 RPM
SRP007412_liver	0.00 RPM	64.39 RPM
SRP007412_testis	0.05 RPM	49.99 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_342 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	1:86472184..86473003
ENCFF001YJZ	POLR2A	1:86470627..86472950
ENCFF001YKA	POLR2A	1:86470824..86472793

EST

No EST(s) were mapped for retro_mmus_342 retrocopy.

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_77174	319 libraries	489 libraries	256 libraries	8 libraries	0 libraries

The graphical summary, for retro_mmus_342 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_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Gorilla gorilla	ENSGGOG00000005502	9 retrocopies	retro_ggor_1416, retro_ggor_1663, retro_ggor_178, retro_ggor_1925, retro_ggor_2661, retro_ggor_2886, retro_ggor_3073, retro_ggor_46, retro_ggor_866,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Mus musculus	ENSMUSG00000058600	21 retrocopies	retro_mmus_1048, retro_mmus_1102, retro_mmus_1276, retro_mmus_1434, retro_mmus_1439, retro_mmus_1586, retro_mmus_2059, retro_mmus_2273, retro_mmus_2728, retro_mmus_2828, retro_mmus_3179, retro_mmus_3286, retro_mmus_342 , retro_mmus_3465, retro_mmus_3573, retro_mmus_3583, retro_mmus_3681, retro_mmus_3691, retro_mmus_569, retro_mmus_789, retro_mmus_892,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Pongo abelii	ENSPPYG00000018774	4 retrocopies	retro_pabe_1605, retro_pabe_178, retro_pabe_2846, retro_pabe_8,
Sus scrofa	ENSSSCG00000006081	6 retrocopies	retro_sscr_100, retro_sscr_1211, retro_sscr_778, retro_sscr_782, retro_sscr_876, retro_sscr_963,