RetrogeneDB ID: retro_mmus_297

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:14865071..14865962(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl5
• Ensembl ID: ENSMUSG00000058558
• Aliases: Rpl5, U21RNA
• Description: ribosomal protein L5 [Source:MGI Symbol;Acc:MGI:102854]

Sequence

>retro_mmus_297
ATGGGGTTTGTGAAAGTTATCAAGAATAAGGCCTACTTTAAAAGATACCAAGTGAGATTTCAAAGGCGGCGAGAGGGTAA
AACTGACTACTATGCTCGAAAACGATTGGTGATCCAGGACAAGAATAAGTACAACACACCCAAATATAGGATGATAGTTC
GTGTAACTAACAGAGATATCATCTGCCAGATTGCATATGCCCGTATAGAAGGGGATATGATCGTCTGTGCAGCATATGCA
CATGAACTTCCAAAATATGGTGTGAAAGTTGGCCTGACAAATTATGCTGCAGCCTATTGCACTGGCCTGCTGCTGGCCCG
CAGGCTTCTGAATAGGTTTGGCATGGACAAGATCTATGAAGGCCAAGTGGAGGTGAATGGAGGTGAATACAATGTGGAAA
GCATTGACGGTCAGCCTGGTGCCTTCACTTGCTATCTGGATGCAGGTCTTGCCCGAACTACAACTGGCAATAAAGTTTTT
GGGGCCCTGAAGGGAGCTGTGGATGGAGGCTTGTCTATCCCTCATAGTACTAAACGATTCCCTGGTTATGACTCTGAAAG
CAAGGTGTTCAATGCAGAGGTACATCGGAAGCACATCATGGGTCAAAATGTGGCAGACTACATGTGCTACCTAATGGAGG
AAGATGAAGATGCGTATAAGAAACAGTTCTCTCAGTACATCAAGAACAATGTAACTCCAGACAAGATGGAGGAGATGTAT
AAGAAAGCTCATGCTGCTATCCGAGAGAATCCAGTCTATGAGAAGAAGCCCAAGAGAGAAGTGAAGAAGAAAAGGTGGAA
TCGTCCCAAAATGTCTCTTGCCCAGAAGAAAGACCGGGTTGCTCAAAAGAAGGCAAGCTTCCTCAGAGCTCAGGAAAGGG
CTGCTGAAAGC

Alignment

ORF - retro_mmus_297 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
          MGFVKV.KNKAYFKRYQVRF.RRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
Retrocopy MGFVKVIKNKAYFKRYQVRFQRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE

Parental  GDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPG
          GDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPG
Retrocopy GDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPG

Parental  AFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRY
          AFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESK.FNAEVHRKHIMGQNVADYM.Y
Retrocopy AFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKVFNAEVHRKHIMGQNVADYMCY

Parental  LMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRV
          LMEEDEDAYKKQFSQYIKNNVTPD.MEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRV
Retrocopy LMEEDEDAYKKQFSQYIKNNVTPDKMEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRV

Parental  AQKKASFLRAQERAAES
          AQKKASFLRAQERAAES
Retrocopy AQKKASFLRAQERAAES

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	0.12 RPM	46.80 RPM
SRP007412_cerebellum	0.13 RPM	34.26 RPM
SRP007412_heart	0.12 RPM	57.28 RPM
SRP007412_kidney	0.06 RPM	78.35 RPM
SRP007412_liver	0.11 RPM	59.15 RPM
SRP007412_testis	0.14 RPM	29.04 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_297 was not detected

EST

No EST(s) were mapped for retro_mmus_297 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_70063	130 libraries	249 libraries	456 libraries	159 libraries	78 libraries

The graphical summary, for retro_mmus_297 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_297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009878	5 retrocopies	retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus	ENSBTAG00000002026	2 retrocopies	retro_btau_120, retro_btau_67,
Equus caballus	ENSECAG00000021065	1 retrocopy	retro_ecab_654,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Mustela putorius furo	ENSMPUG00000004150	6 retrocopies	retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus	ENSMUSG00000058558	11 retrocopies	retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297 , retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Oryctolagus cuniculus	ENSOCUG00000010089	2 retrocopies	retro_ocun_265, retro_ocun_54,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pteropus vampyrus	ENSPVAG00000015117	4 retrocopies	retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus	ENSRNOG00000023529	6 retrocopies	retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Sus scrofa	ENSSSCG00000006899	2 retrocopies	retro_sscr_149, retro_sscr_219,
Tupaia belangeri	ENSTBEG00000010560	5 retrocopies	retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus	ENSTTRG00000013097	5 retrocopies	retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,