RetrogeneDB ID: retro_mmus_654

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:71799235..71799847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psma6
• Ensembl ID: ENSMUSG00000021024
• Aliases: Psma6, IOTA
• Description: proteasome (prosome, macropain) subunit, alpha type 6 [Source:MGI Symbol;Acc:MGI:1347006]

Sequence

>retro_mmus_654
ATGTCCTATGGTTCCAGTGCTGGTTTTTGACCTTCACATTACTATTTTTTCTCCTGAAGGCCAACTCTACCAAGTAGAAT
GTGCTTTTAAGATTATTAACCAAGGTGGACTTACATCTGTCACTGTCAGAGGAAAGGACTGTGCAGTTATCGTCAAACAG
AAGAAAGTACCTGTCAAATTGCTAGATTCTAGCATGGTGTCTAATTTGTTCGGGATGACTGTAAGCATTGGTTGTGTAGT
GACAGGTGTGACAGCTGACAGTAGACCCCAGGTACAGAGAGCACACTGTGAGGCAGATAATTGGAAATACAAATATGGTT
ATGAGATTCCTATGGGCATGCTATATAAAAAGAATTGGTGATATTTCTCAAGTCAACACACAGAATGCTGAAATGAGGCT
GCTTGGTTGCTGTATGATTTTAATTGGTATAGATGAAGAACAAGGTCCTCATGTGTTCGGGTGTGACCCTGCAGGCTGCA
ACTGTGACTTTAAAGCCCACATGAGCAGGAGTTAAACAAACAGAGTCAACCAGCTTTCTCAAAAAAAAAAAAGTGAAAAA
GAAATTTTATTGGACATTTGGACAGCAGAAACTGCAATTCCATGCCTGTCTG

Alignment

ORF - retro_mmus_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 82.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGF-DRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHL
          MS.GSSAGF.D.HITIFSPEG.LYQVE.AFK.INQGGLTSV.VRGKDCAVIV.QKKVP.KLLDSS.V..L
Retrocopy MSYGSSAGF>DLHITIFSPEGQLYQVECAFKIINQGGLTSVTVRGKDCAVIVKQKKVPVKLLDSSMVSNL

Parental  FKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDML-CKRIADISQVYTQNAEMRPLGCCM
          F..T.SIGCV.TG.TADSR.QVQRA..EA.NWKYKYGYEIP..ML..KRI.DISQV.TQNAEMR.LGCCM
Retrocopy FGMTVSIGCVVTGVTADSRPQVQRAHCEADNWKYKYGYEIPMGML>IKRIGDISQVNTQNAEMRLLGCCM

Parental  ILIGIDEEQGPQVYKCDPAGYYCGFKA-TAAGVKQTESTSFL-EKKVKKKFDWTFEQTVETAITCL
          ILIGIDEEQGP.V..CDPAG..C.FKA.T.AGVKQTESTSFL.......KF.WTF.Q.......CL
Retrocopy ILIGIDEEQGPHVFGCDPAGCNCDFKA>T*AGVKQTESTSFLXXXXXXXKFYWTFGQQKLQFHACL

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	0.02 RPM	59.53 RPM
SRP007412_cerebellum	0.04 RPM	48.55 RPM
SRP007412_heart	0.00 RPM	60.92 RPM
SRP007412_kidney	0.02 RPM	65.83 RPM
SRP007412_liver	0.00 RPM	69.09 RPM
SRP007412_testis	0.00 RPM	304.99 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_654 was not detected

EST

No EST(s) were mapped for retro_mmus_654 retrocopy.

TSS

No TSS is located nearby retro_mmus_654 retrocopy 5' end.

Lab

retro_mmus_654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_654 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1724

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013409	2 retrocopies	retro_cfam_1581, retro_cfam_743,
Echinops telfairi	ENSETEG00000004892	1 retrocopy	retro_etel_1775,
Felis catus	ENSFCAG00000026276	1 retrocopy	retro_fcat_973,
Homo sapiens	ENSG00000100902	2 retrocopies	retro_hsap_1228, retro_hsap_4923,
Macropus eugenii	ENSMEUG00000016537	1 retrocopy	retro_meug_1217,
Microcebus murinus	ENSMICG00000000083	4 retrocopies	retro_mmur_104, retro_mmur_165, retro_mmur_752, retro_mmur_80,
Myotis lucifugus	ENSMLUG00000010228	1 retrocopy	retro_mluc_822,
Macaca mulatta	ENSMMUG00000016544	1 retrocopy	retro_mmul_343,
Mustela putorius furo	ENSMPUG00000016288	1 retrocopy	retro_mputfur_1089,
Mus musculus	ENSMUSG00000021024	1 retrocopy	retro_mmus_654 ,
Otolemur garnettii	ENSOGAG00000008492	10 retrocopies	retro_ogar_1273, retro_ogar_1397, retro_ogar_1928, retro_ogar_1950, retro_ogar_2021, retro_ogar_2073, retro_ogar_2274, retro_ogar_2488, retro_ogar_2521, retro_ogar_3089,
Pan troglodytes	ENSPTRG00000006264	2 retrocopies	retro_ptro_3297, retro_ptro_844,
Rattus norvegicus	ENSRNOG00000007114	4 retrocopies	retro_rnor_1724, retro_rnor_1960, retro_rnor_854, retro_rnor_924,
Tupaia belangeri	ENSTBEG00000011241	17 retrocopies	retro_tbel_1304, retro_tbel_1415, retro_tbel_1789, retro_tbel_2028, retro_tbel_2466, retro_tbel_2519, retro_tbel_3227, retro_tbel_3280, retro_tbel_3535, retro_tbel_4181, retro_tbel_4183, retro_tbel_4357, retro_tbel_4465, retro_tbel_4495, retro_tbel_509, retro_tbel_602, retro_tbel_725,