RetrogeneDB ID: retro_mmus_2562

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:41342254..41342931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl7
• Ensembl ID: ENSMUSG00000043716
• Aliases: Rpl7, Rpl7a, Surf-3
• Description: ribosomal protein L7 [Source:MGI Symbol;Acc:MGI:98073]

Sequence

>retro_mmus_2562
AAGAATTTCGCAGAGTTGAAGGTGAAGCGCCTGAGGAAGAAGTTTGCCCTGAAGACACTTCGAAAGGCAAGGAGGAAGCT
CATCTATGAGAAGGCAAAACACTATCACAAGGAGTACAGGCAGATGTACCGCACTGAGATCAGATGGCCAGGATGGCAAG
GGAAGCTGGGAGCTTCTATGTGCCCGAAGAACCAAAACTGGCCTTTGTCATCAGAATCCGAGGTATCAATGGAGTAAGCC
CAAAGGTTCGGAAGGTTCTGCAGCTCCTTCGTCTTCGACAGATCTTCAATGGCACCTTTGCTAAGCTCAACAAGGCTTCA
ATCAACATGCTGCGGATTGTGGAACCATACATTGCATGGGGGTACCCCAACCTGAAGTCAGTAAACGAGTTCATCTACAA
GCGAGGCTACGGCAAAATCAACAAGAAGCCAATTGCCTTGACAGATAATTCCTTGATTGCTCGGTCTCTTGGTAAGTTTG
GCATCATCTGCATGGAGGATCTAATGCATGAGATCTATACAGTTGGGAAACGCTTCAAGGAAGCAACTAACTTCCTGTGG
CCCTTCAAATTATGTTCCCCACGAGGTGGAATGAAGAAAAAGACAACTCATGTTGTAGAAGGTGGAGATACTGGCATGAG
AGAAGACCAGATAAACAGGCTTATTAGACGGATGAAC

Alignment

ORF - retro_mmus_2562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.83 %
• Parental protein coverage: 83.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNFAELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIR-MARMARKAGNFYVPAEPKLAF
          .NFAELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIR.MARMAR.AG.FYVP.EPKLAF
Retrocopy KNFAELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIR<MARMAREAGSFYVPEEPKLAF

Parental  VIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGK
          VIRIRGINGVSPKVRKVLQLLRLRQIFNGTF.KLNKASINMLRIVEPYIAWGYPNLKSVNE.IYKRGYGK
Retrocopy VIRIRGINGVSPKVRKVLQLLRLRQIFNGTFAKLNKASINMLRIVEPYIAWGYPNLKSVNEFIYKRGYGK

Parental  INKKRIALTDNSLIARSLGKFGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGG
          INKK.IALTDNSLIARSLGKFGIICMEDL.HEIYTVGKRFKEA.NFLWPFKL.SPRGGMKKKTTH.VEGG
Retrocopy INKKPIALTDNSLIARSLGKFGIICMEDLMHEIYTVGKRFKEATNFLWPFKLCSPRGGMKKKTTHVVEGG

Parental  DAGNREDQINRLIRRMN
          D.G.REDQINRLIRRMN
Retrocopy DTGMREDQINRLIRRMN

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	108.26 RPM
SRP007412_cerebellum	0.00 RPM	87.10 RPM
SRP007412_heart	0.03 RPM	118.08 RPM
SRP007412_kidney	0.08 RPM	156.36 RPM
SRP007412_liver	0.00 RPM	136.76 RPM
SRP007412_testis	0.00 RPM	77.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2562 was not detected

EST

No EST(s) were mapped for retro_mmus_2562 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_114059	285 libraries	413 libraries	338 libraries	29 libraries	7 libraries

The graphical summary, for retro_mmus_2562 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_2562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 113 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020139	22 retrocopies	retro_btau_1088, retro_btau_1231, retro_btau_1367, retro_btau_1381, retro_btau_1422, retro_btau_1434, retro_btau_1468, retro_btau_1548, retro_btau_1559, retro_btau_1616, retro_btau_1627, retro_btau_1784, retro_btau_1814, retro_btau_304, retro_btau_426, retro_btau_622, retro_btau_668, retro_btau_730, retro_btau_750, retro_btau_758, retro_btau_863, retro_btau_879,
Callithrix jacchus	ENSCJAG00000007686	1 retrocopy	retro_cjac_105,
Equus caballus	ENSECAG00000009188	1 retrocopy	retro_ecab_35,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Macaca mulatta	ENSMMUG00000005141	1 retrocopy	retro_mmul_129,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Mus musculus	ENSMUSG00000043716	15 retrocopies	retro_mmus_1232, retro_mmus_1345, retro_mmus_1631, retro_mmus_2549, retro_mmus_2562 , retro_mmus_2798, retro_mmus_3259, retro_mmus_3305, retro_mmus_3440, retro_mmus_3547, retro_mmus_3552, retro_mmus_3685, retro_mmus_561, retro_mmus_595, retro_mmus_708,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Otolemur garnettii	ENSOGAG00000003903	2 retrocopies	retro_ogar_15, retro_ogar_225,
Rattus norvegicus	ENSRNOG00000006992	27 retrocopies	retro_rnor_1018, retro_rnor_1174, retro_rnor_1222, retro_rnor_1233, retro_rnor_1307, retro_rnor_1388, retro_rnor_1466, retro_rnor_1580, retro_rnor_1745, retro_rnor_1916, retro_rnor_1944, retro_rnor_2025, retro_rnor_2028, retro_rnor_2100, retro_rnor_2247, retro_rnor_2304, retro_rnor_2347, retro_rnor_2531, retro_rnor_2715, retro_rnor_2765, retro_rnor_2814, retro_rnor_2824, retro_rnor_530, retro_rnor_666, retro_rnor_911, retro_rnor_929, retro_rnor_977,
Tupaia belangeri	ENSTBEG00000002301	1 retrocopy	retro_tbel_2042,
Tarsius syrichta	ENSTSYG00000006100	25 retrocopies	retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,