RetrogeneDB ID: retro_mmus_462

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:81741987..81742969(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000087008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Plscr1
• Ensembl ID: ENSMUSG00000032369
• Aliases: Plscr1, MmTRA1a, MmTRA1b, Nor1, Tra1, Tra1a, Tra1b, Tras1, Tras2
• Description: phospholipid scramblase 1 [Source:MGI Symbol;Acc:MGI:893575]

Sequence

>retro_mmus_462
ATGGAAAACCACAGCAAGCAAACTGAGGCTCCCACCCGGAAGAACATATATGCCAGCTTGGTATCCCCCTCTGTATCCAC
CAGCAGCTTTCCAAGGACCTTCATACCGTGCTGCTTACTCCATACCCCAGGCTGGCTACCAAGGGCCTCCGGGCCCCTAT
CCAGGGCCCCAACCTGGTTACCCAGTCCCACCAGGAGGTTATGCAGGTGGTGGCCCTAGTGGCTTTCCTGTCCAAAATCA
GCCAGCATGTAATCATCCAGGTGGGCCTGGGGGGACCCCATGGATGCCAGCCCCCCCTCCTCCACTGAACTGTCCACCAG
GGCTGGAATACTTAGCTCAGATTGATCAGCTTCTGGTTCATCAGCAAATTGAGCTTCTGGAAGTCTTAACAGGCTTTGAA
ACAAATAACAAATATGAAATCAAGAACAGCCTCGGGCAGAGAGTTTACTTTGCAGTGGAAGATACTGACTGCTGTACCCG
AAACTGCCGTGGGGCGTCTAGACCTTTCACCTTGAGGATCCTGGATAACCTGGGCCGAGAAGTCATGACTCTGGAGAGAC
CTCTGAGATGCAGTTACTGCTGCTTCCCCTGCTGCCTCCAGGAGATAGAAATCCAGGCTCCTCCTGGGGTGCCAGTAGGT
TATGTAACTCAGACCTGGCACCCATGTCTGCCCAAGTTCACTCTCCAAAATGAGAAGAAGCAGGATGTTCTGAAAGTTGT
TGGTTCGTGTGTTGTGTGTAGCTGCTGTTCCGACATTGACTTTGAGCTCAAATCTCTAGATGAAGAATCAGTAGTTGGCA
AAATTTCTAAGCAGTGGTCTGGTTTTGTGAGAGAGGCCTTCACGGATGCAGACAATTTTGGGGTCCAGTTCCCGCTAGAC
CTGGATGTGAAGATGAAAGCTGTGATGCTTGGTGCTTGTTTCCTCATAGATTTCACGTTTTTTGAAAGAACTGGAAACGA
GGAACAAAGATCAGGAGCATGG

Alignment

ORF - retro_mmus_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.43 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENHSKQTEA-PHPGTYMPAGYPPPYPPAAFQGPSDHAAYPIPQAGYQGPPGPYPGPQPGYPVPPGGYAG
          MENHSKQTEA.P...TYMPA.YPP.YPPAAFQGPS..AAY.IPQAGYQGPPGPYPGPQPGYPVPPGGYAG
Retrocopy MENHSKQTEA>PPGRTYMPAWYPPLYPPAAFQGPSYRAAYSIPQAGYQGPPGPYPGPQPGYPVPPGGYAG

Parental  GGPSGFPVQNQPAYNHPGGPGGTPWMPAPPPPLNCPPGLEYLAQIDQLLVHQQIELLEVLTGFETNNKYE
          GGPSGFPVQNQPA.NHPGGPGGTPWMPAPPPPLNCPPGLEYLAQIDQLLVHQQIELLEVLTGFETNNKYE
Retrocopy GGPSGFPVQNQPACNHPGGPGGTPWMPAPPPPLNCPPGLEYLAQIDQLLVHQQIELLEVLTGFETNNKYE

Parental  IKNSLGQRVYFAVEDTDCCTRNCCGASRPFTLRILDNLGREVMTLERPLRCSSCCFPCCLQEIEIQAPPG
          IKNSLGQRVYFAVEDTDCCTRNC.GASRPFTLRILDNLGREVMTLERPLRCS.CCFPCCLQEIEIQAPPG
Retrocopy IKNSLGQRVYFAVEDTDCCTRNCRGASRPFTLRILDNLGREVMTLERPLRCSYCCFPCCLQEIEIQAPPG

Parental  VPVGYVTQTWHPCLPKFTLQNEKKQDVLKVVGPCVVCSCCSDIDFELKSLDEESVVGKISKQWSGFVREA
          VPVGYVTQTWHPCLPKFTLQNEKKQDVLKVVG.CVVCSCCSDIDFELKSLDEESVVGKISKQWSGFVREA
Retrocopy VPVGYVTQTWHPCLPKFTLQNEKKQDVLKVVGSCVVCSCCSDIDFELKSLDEESVVGKISKQWSGFVREA

Parental  FTDADNFGIQFPLDLDVKMKAVMLGACFLIDFMFFERTGNEEQRSGAW
          FTDADNFG.QFPLDLDVKMKAVMLGACFLIDF.FFERTGNEEQRSGAW
Retrocopy FTDADNFGVQFPLDLDVKMKAVMLGACFLIDFTFFERTGNEEQRSGAW

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	1.05 RPM
SRP007412_cerebellum	0.00 RPM	2.34 RPM
SRP007412_heart	0.03 RPM	7.56 RPM
SRP007412_kidney	0.12 RPM	25.85 RPM
SRP007412_liver	0.03 RPM	10.76 RPM
SRP007412_testis	0.00 RPM	0.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_462 was not detected

EST

No EST(s) were mapped for retro_mmus_462 retrocopy.

TSS

No TSS is located nearby retro_mmus_462 retrocopy 5' end.

Lab

retro_mmus_462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_462 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000027005	1 retrocopy	retro_fcat_797,
Myotis lucifugus	ENSMLUG00000008749	1 retrocopy	retro_mluc_1779,
Monodelphis domestica	ENSMODG00000021248	2 retrocopies	retro_mdom_1443, retro_mdom_1597,
Mus musculus	ENSMUSG00000019461	1 retrocopy	retro_mmus_1154,
Mus musculus	ENSMUSG00000032369	1 retrocopy	retro_mmus_462 ,